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Data Deposition Example 2:
Sample Data Items

Example 2 presents a incomplete deposition entry using the structure 1KIP.

TO BEGIN

To begin this example, select the BEGIN EXAMPLE 2 button. A coordinate file containing only the SCALE cards, CRYST card, and coordinates has already been loaded for you.

DATA EXAMPLES

Choose the first category, Contact authors, from the left-hand (Categories) frame. At any time, EXAMPLES or HELP can be obtained by selecting the appropriate buttons. This information will appear in lower right frame of your browser. For this example assume that you are the contact person for the deposition and enter the appropriate information in the table in the frame at the center right of the browser. Press SAVE when you have finished entering the information.

Continue through the categories, entering the information below, always saving each frame after you have entered the information. Since this is an example taken from an actual file, you will not be filling all of the fields available in the deposition tool, but primarily those supplied originally by the author. At any time you may preview the entire entry by pressing the PREVIEW ENTRY BUTTON or display the information entered in a category as a table (in the bottom frame) by pressing the DISPLAY AS TABLE BUTTON.

 

Select the Release Status category.

Choose the manner in which you would like the deposited data to be released. Note that unless you select otherwise, your data will be RELEASED IMMEDIATELY. In this example case this option is fine.

 

Select the Title category.

For the deposition title enter:

FV Mutant Y(B 32) A (VH domain) of Mouse Monoclonal Antibody FV Mutant Y (B 32) A (VH Domain) of Mouse Monoclonal Antibody D1.3 Complexed With Hen Egg White Lysozyme.

 

Select the Related Entries category.

For Database name enter PDB from the pull-down menu.

Enter 1KIQ for Database ID code.

Repeat this in the second row, entering the PDB ID 1KIR.

 

Select the Citation Authors category.

For the primary citation, enter the following author’s names, each on a separate line:

Fields, B.A.

Goldbaum, F.A.

Dall'Acqua, W.

Malchiodi, E.L.

Cauerhff, A.

Schwarz, F.P.

Ysern, X.

Poljak, R.J.

Mariuzza, R.A.

After you have entered the first five authors, save the category and select the Citation Authors category again. This will provide you with additional lines for the remaining authors.

Press SAVE

 

Select the Citation category.

For the primary citation, enter the following information

Year: 1996

Journal abbreviation: Biochemistry (from the pull-down menu)

Journal volume: 35

First page: 15494

Last page: 15503

Title: Hydrogen Bonding and Solvent Structure in an Antigen-Antibody Interface. Crystal Structures and Thermodynamic Characterization of Three Fv Mutants Complexed with Lysozyme.

Press SAVE

 

Select the Chemical Description category.

Enter "monoclonal antibody" for the first and second entities under Entity description. Enter "lysozyme" for the third entity. Enter water as the fourth entity.

Press SAVE

 

Select the Chemical Details category.

Enter "Y(B 32)A (VH DOMAIN)" under Specific mutation for the second entity (since the mutation occurs in chain B, which is the second entity).

Press SAVE

 

Select the Sequence category.

Enter the following information:

For entity 1:

One-letter sequence code:

DIVLTQSPASLSASVGETVTITCRASGNIHNYLAWYQQKQGKSPQLLVYYTTTLADGVPSRFSGS GSGTQYSLKINSLQPEDFGSYYCQHFWSTPRTFGGGTKLEIK

Chain identifiers: A

Sequence database name: PIR

Sequence database code: S19112

Beginning sequence position:1

Ending sequence position: 107

For entity 2:

One-letter sequence code:

QVQLQESGPGLVAPSQSLSITCTVSGFSLTGAGVNWVRQPPGKGLEWLGMIWGDGNTDYNSALK SRLSISKDNSKSQVFLKMNSLHTDDTARYYCARERDYRLDYWGQGTTLTVSS

Chain identifiers: B

Sequence database name: GB

Sequence database code: L43544

Beginning sequence position:133

Ending sequence position: 248

 

For entity 3:

One-letter sequence code:

KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCN DGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL

Chain identifiers: C

Sequence database name: SWS

Sequence database code: P00698

Beginning sequence position:19

Ending sequence position: 147

Press SAVE

 

Select the Natural Source category.

For entity 3 (skip down to the third table) enter "Chicken" under Natural source.

Press SAVE

 

Select the Genetically Manipulated Source category.

For entities 1 and 2, enter "Mouse" under Source of gene and "Escherichia Coli" under Expression system name. You may skip the Synthetic Source Category.

Press SAVE

 

You may skip the Keywords, Biological features, Crystallization Conditions categories as this information was not provided in the original deposition.

 

Select the Unit Cell category.

Enter the following information:

Length a: 129.230

Length b: 60.440

Length c: 56.630

Angle alpha: 90.00

Angle beta: 119.05

Angle gamma: 90.00

Press SAVE

 

Select the Space Group category.

Choose C2 from the pull-down menu for Space-group name.

Press SAVE

 

Select the Crystals category.

Chose 1 for Number of crystals.

Press SAVE

 

Select the Radiation Source category.

For Diffraction experiment 1, enter 1.5418 under Wavelength. (Other information in this category was not provided in the original deposition).

Press SAVE

 

Select the Radiation Detector category.

For Diffraction experiment 1, enter the following information:

Detector: MULTIWIRE

Detector type: SIEMENS

Data collection date: 1994-10-05

Press SAVE

 

You may skip the Conditions category as this information was not provided in the original deposition.

 

Select the Reflection Details category.

Enter the following information:

Observed criterion sigma(I): 0.0

Number reflections (observed): 20023

Percent possible (observed): 91.3

R-merge I (observed): 0.086

Redundancy: 2.5

Press SAVE

 

You may skip the High Resolution Shell category as this information was not provided in the original deposition.

 

Select the Data Parameters category.

Enter the following information:

Resolution (high): 2.10

Resolution (low): 7.0

Cut-off sigma(F): 2.0

Number reflections (observed): 15354

Percent reflections observed: 70.3

R-factor (R-work): 0.162

Press SAVE

 

Select the RMS Deviations category.

Enter the following information:

x_bond_d: 0.015

x_angle_deg: 1.9

Press SAVE

 

Select the Programs category.

Enter the following information:

Data collection: XENGEN

Data reduction: XENGEN

Structure refinement: X-PLOR 3.1

Press SAVE

 

Press DEPOSIT, and you will be given a measure of the completeness of the entry and shown the deposition in tabular format. You may choose to either return to the input tool to edit any entered information or you may press the Deposit Now button to complete the deposition. This will not count as an actual deposition to the PDB.

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