3D19 | pdb_00003d19

Crystal structure of a conserved metalloprotein from Bacillus cereus

PDB DOI: https://doi.org/10.2210/pdb3D19/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Bacillus cereus G9241
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2008-05-05 Released: 2008-07-08
Deposition Author(s): Bonanno, J.B., Patskovsky, Y., Freeman, J., Bain, K.T., Chang, S., Ozyurt, S., Smith, D., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.268 (Depositor), 0.245 (DCC)
R-Value Work:
0.206 (Depositor)
R-Value Observed:
0.210 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.6 of the entry. See complete history.

Literature

Crystal structure of a conserved metalloprotein from Bacillus cereus.

Bonanno, J.B., Patskovsky, Y., Freeman, J., Bain, K.T., Chang, S., Ozyurt, S., Smith, D., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 200.51 kDa
Atom Count: 13,109
Modeled Residue Count: 1,558
Deposited Residue Count: 1,698
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Conserved metalloprotein	A, B, C, D, E A, B, C, D, E, F	283	Bacillus cereus G9241	Mutation(s): 5 Gene Names: BCE_G9241_1042

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain N [auth D] SDF format, chain P [auth E] SDF format, chain R [auth F] SDF format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain N [auth D] MOL2 format, chain P [auth E] MOL2 format, chain R [auth F] MOL2 format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain L [auth C] mmCIF format, chain N [auth D] mmCIF format, chain P [auth E] mmCIF format, chain R [auth F] mmCIF format, chain H [auth A]	H [auth A] J [auth B] L [auth C] N [auth D] P [auth E] H [auth A], J [auth B], L [auth C], N [auth D], P [auth E], R [auth F]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain P [auth E] Focus chain R [auth F] Interactions & Density Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain P [auth E] Focus chain R [auth F]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain M [auth D] SDF format, chain Q [auth F] SDF format, chain O [auth E] SDF format, chain I [auth B] SDF format, chain G [auth A] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] MOL2 format, chain Q [auth F] MOL2 format, chain O [auth E] MOL2 format, chain I [auth B] MOL2 format, chain G [auth A] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D] mmCIF format, chain Q [auth F] mmCIF format, chain O [auth E] mmCIF format, chain I [auth B] mmCIF format, chain G [auth A]	G [auth A] I [auth B] K [auth C] M [auth D] O [auth E] G [auth A], I [auth B], K [auth C], M [auth D], O [auth E], Q [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E] Focus chain Q [auth F] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E] Focus chain Q [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.268 (Depositor), 0.245 (DCC)
R-Value Work: 0.206 (Depositor)
R-Value Observed: 0.210 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.825	α = 90
b = 136.378	β = 102.84
c = 87.06	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
DENZO	data reduction
SHELXCD	phasing
SHELXE	model building

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-07-08

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2008-07-08
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: 2018-11-14
Changes: Data collection, Structure summary
Version 1.4: 2021-02-03
Changes: Database references, Derived calculations, Structure summary
Version 1.5: 2021-10-20
Changes: Database references
Version 1.6: 2024-10-09
Changes: Data collection, Structure summary