3DBY | pdb_00003dby

Crystal structure of uncharacterized protein from Bacillus cereus G9241 (CSAP Target)

PDB DOI: https://doi.org/10.2210/pdb3DBY/pdb

Classification: structural genomics, unknown function
Organism(s): Bacillus cereus G9241
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-06-02 Released: 2008-07-29
Deposition Author(s): Ramagopal, U.A., Bonanno, J.B., Ozyurt, S., Freeman, J., Wasserman, S., Hu, S., Groshong, C., Rodgers, L., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.258 (Depositor), 0.212 (DCC)
R-Value Work:
0.198 (Depositor)
R-Value Observed:
0.201 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of uncharacterized protein from Bacillus cereus G9241

Ramagopal, U.A., Bonanno, J.B., Ozyurt, S., Freeman, J., Wasserman, S., Hu, S., Groshong, C., Rodgers, L., Burley, S.K., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 630.72 kDa
Atom Count: 45,580
Modeled Residue Count: 5,238
Deposited Residue Count: 5,380
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized protein	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T	269	Bacillus cereus G9241	Mutation(s): 0 Gene Names: BCE_G9241_0798

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain FB [auth R] SDF format, chain Y [auth B] MOL2 format, chain FB [auth R] MOL2 format, chain Y [auth B] mmCIF format, chain FB [auth R] mmCIF format, chain Y [auth B]	FB [auth R], Y [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain FB [auth R] Focus chain Y [auth B] Interactions & Density Focus chain FB [auth R] Focus chain Y [auth B]
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain AB [auth P] SDF format, chain BA [auth D] SDF format, chain BB [auth Q] SDF format, chain CB [auth Q] SDF format, chain DB [auth R] SDF format, chain EA [auth E] SDF format, chain FA [auth F] SDF format, chain GA [auth F] SDF format, chain HA [auth G] SDF format, chain HB [auth S] SDF format, chain IA [auth G] SDF format, chain IB [auth T] SDF format, chain JA [auth H] SDF format, chain JB [auth T] SDF format, chain KA [auth H] SDF format, chain LA [auth I] SDF format, chain NA [auth J] SDF format, chain OA [auth J] SDF format, chain PA [auth K] SDF format, chain QA [auth K] SDF format, chain RA [auth L] SDF format, chain SA [auth L] SDF format, chain TA [auth M] SDF format, chain U [auth A] SDF format, chain UA [auth M] SDF format, chain V [auth A] SDF format, chain VA [auth N] SDF format, chain W [auth B] SDF format, chain WA [auth N] SDF format, chain X [auth B] SDF format, chain XA [auth O] SDF format, chain YA [auth O] SDF format, chain Z [auth C] SDF format, chain ZA [auth P] SDF format, chain MA [auth I] SDF format, chain GB [auth S] SDF format, chain EB [auth R] SDF format, chain DA [auth E] SDF format, chain CA [auth D] MOL2 format, chain AA [auth C] MOL2 format, chain AB [auth P] MOL2 format, chain BA [auth D] MOL2 format, chain BB [auth Q] MOL2 format, chain CB [auth Q] MOL2 format, chain DB [auth R] MOL2 format, chain EA [auth E] MOL2 format, chain FA [auth F] MOL2 format, chain GA [auth F] MOL2 format, chain HA [auth G] MOL2 format, chain HB [auth S] MOL2 format, chain IA [auth G] MOL2 format, chain IB [auth T] MOL2 format, chain JA [auth H] MOL2 format, chain JB [auth T] MOL2 format, chain KA [auth H] MOL2 format, chain LA [auth I] MOL2 format, chain NA [auth J] MOL2 format, chain OA [auth J] MOL2 format, chain PA [auth K] MOL2 format, chain QA [auth K] MOL2 format, chain RA [auth L] MOL2 format, chain SA [auth L] MOL2 format, chain TA [auth M] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth M] MOL2 format, chain V [auth A] MOL2 format, chain VA [auth N] MOL2 format, chain W [auth B] MOL2 format, chain WA [auth N] MOL2 format, chain X [auth B] MOL2 format, chain XA [auth O] MOL2 format, chain YA [auth O] MOL2 format, chain Z [auth C] MOL2 format, chain ZA [auth P] MOL2 format, chain MA [auth I] MOL2 format, chain GB [auth S] MOL2 format, chain EB [auth R] MOL2 format, chain DA [auth E] MOL2 format, chain CA [auth D] mmCIF format, chain AA [auth C] mmCIF format, chain AB [auth P] mmCIF format, chain BA [auth D] mmCIF format, chain BB [auth Q] mmCIF format, chain CB [auth Q] mmCIF format, chain DB [auth R] mmCIF format, chain EA [auth E] mmCIF format, chain FA [auth F] mmCIF format, chain GA [auth F] mmCIF format, chain HA [auth G] mmCIF format, chain HB [auth S] mmCIF format, chain IA [auth G] mmCIF format, chain IB [auth T] mmCIF format, chain JA [auth H] mmCIF format, chain JB [auth T] mmCIF format, chain KA [auth H] mmCIF format, chain LA [auth I] mmCIF format, chain NA [auth J] mmCIF format, chain OA [auth J] mmCIF format, chain PA [auth K] mmCIF format, chain QA [auth K] mmCIF format, chain RA [auth L] mmCIF format, chain SA [auth L] mmCIF format, chain TA [auth M] mmCIF format, chain U [auth A] mmCIF format, chain UA [auth M] mmCIF format, chain V [auth A] mmCIF format, chain VA [auth N] mmCIF format, chain W [auth B] mmCIF format, chain WA [auth N] mmCIF format, chain X [auth B] mmCIF format, chain XA [auth O] mmCIF format, chain YA [auth O] mmCIF format, chain Z [auth C] mmCIF format, chain ZA [auth P] mmCIF format, chain MA [auth I] mmCIF format, chain GB [auth S] mmCIF format, chain EB [auth R] mmCIF format, chain DA [auth E] mmCIF format, chain CA [auth D]	AA [auth C] AB [auth P] BA [auth D] BB [auth Q] CA [auth D] AA [auth C], AB [auth P], BA [auth D], BB [auth Q], CA [auth D], CB [auth Q], DA [auth E], DB [auth R], EA [auth E], EB [auth R], FA [auth F], GA [auth F], GB [auth S], HA [auth G], HB [auth S], IA [auth G], IB [auth T], JA [auth H], JB [auth T], KA [auth H], LA [auth I], MA [auth I], NA [auth J], OA [auth J], PA [auth K], QA [auth K], RA [auth L], SA [auth L], TA [auth M], U [auth A], UA [auth M], V [auth A], VA [auth N], W [auth B], WA [auth N], X [auth B], XA [auth O], YA [auth O], Z [auth C], ZA [auth P]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain AB [auth P] Focus chain BA [auth D] Focus chain BB [auth Q] Focus chain CA [auth D] Focus chain CB [auth Q] Focus chain DA [auth E] Focus chain DB [auth R] Focus chain EA [auth E] Focus chain EB [auth R] Focus chain FA [auth F] Focus chain GA [auth F] Focus chain GB [auth S] Focus chain HA [auth G] Focus chain HB [auth S] Focus chain IA [auth G] Focus chain IB [auth T] Focus chain JA [auth H] Focus chain JB [auth T] Focus chain KA [auth H] Focus chain LA [auth I] Focus chain MA [auth I] Focus chain NA [auth J] Focus chain OA [auth J] Focus chain PA [auth K] Focus chain QA [auth K] Focus chain RA [auth L] Focus chain SA [auth L] Focus chain TA [auth M] Focus chain U [auth A] Focus chain UA [auth M] Focus chain V [auth A] Focus chain VA [auth N] Focus chain W [auth B] Focus chain WA [auth N] Focus chain X [auth B] Focus chain XA [auth O] Focus chain YA [auth O] Focus chain Z [auth C] Focus chain ZA [auth P] Interactions & Density Focus chain AA [auth C] Focus chain AB [auth P] Focus chain BA [auth D] Focus chain BB [auth Q] Focus chain CA [auth D] Focus chain CB [auth Q] Focus chain DA [auth E] Focus chain DB [auth R] Focus chain EA [auth E] Focus chain EB [auth R] Focus chain FA [auth F] Focus chain GA [auth F] Focus chain GB [auth S] Focus chain HA [auth G] Focus chain HB [auth S] Focus chain IA [auth G] Focus chain IB [auth T] Focus chain JA [auth H] Focus chain JB [auth T] Focus chain KA [auth H] Focus chain LA [auth I] Focus chain MA [auth I] Focus chain NA [auth J] Focus chain OA [auth J] Focus chain PA [auth K] Focus chain QA [auth K] Focus chain RA [auth L] Focus chain SA [auth L] Focus chain TA [auth M] Focus chain U [auth A] Focus chain UA [auth M] Focus chain V [auth A] Focus chain VA [auth N] Focus chain W [auth B] Focus chain WA [auth N] Focus chain X [auth B] Focus chain XA [auth O] Focus chain YA [auth O] Focus chain Z [auth C] Focus chain ZA [auth P]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.258 (Depositor), 0.212 (DCC)
R-Value Work: 0.198 (Depositor)
R-Value Observed: 0.201 (Depositor)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 167.808	α = 90
b = 167.808	β = 90
c = 582.661	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-07-29

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2008-07-29
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2021-02-10
Changes: Database references, Derived calculations, Structure summary
Version 1.4: 2024-10-30
Changes: Data collection, Database references, Structure summary