3M6Y | pdb_00003m6y

Structure of 4-hydroxy-2-oxoglutarate aldolase from bacillus cereus at 1.45 a resolution.

PDB DOI: https://doi.org/10.2210/pdb3M6Y/pdb

Classification: LYASE
Organism(s): Bacillus cereus ATCC 14579
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2010-03-16 Released: 2010-04-07
Deposition Author(s): Filippova, E.V., Minasov, G., Shuvalova, L., Kiryukhina, O., Clancy, S., Joachimiak, A., Anderson, F.W., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free:
0.180 (Depositor), 0.196 (DCC)
R-Value Work:
0.152 (Depositor), 0.169 (DCC)
R-Value Observed:
0.153 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Structure of 4-Hydroxy-2-Oxoglutarate Aldolase from Bacillus Cereus at 1.45 A Resolution.

Filippova, E.V., Minasov, G., Shuvalova, L., Kiryukhina, O., Clancy, S., Joachimiak, A., Anderson, W.F.

To be published.

Macromolecule Content

Total Structure Weight: 120.22 kDa
Atom Count: 8,851
Modeled Residue Count: 998
Deposited Residue Count: 1,100
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-Hydroxy-2-oxoglutarate aldolase	A, B, C, D	275	Bacillus cereus ATCC 14579	Mutation(s): 0 Gene Names: 29898472, BC_4844 EC: 4.1.3.16
UniProt
Find proteins for Q812M4 (Bacillus cereus (strain ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NCTC 2599 / NRRL B-3711)) Explore Q812M4 Go to UniProtKB: Q812M4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q812M4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B]	E [auth A], F [auth A], I [auth B], J [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain M [auth C] SDF format, chain N [auth D] SDF format, chain L [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth D] MOL2 format, chain L [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain M [auth C] mmCIF format, chain N [auth D] mmCIF format, chain L [auth B]	G [auth A] H [auth A] K [auth B] L [auth B] M [auth C] G [auth A], H [auth A], K [auth B], L [auth B], M [auth C], N [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.180 (Depositor), 0.196 (DCC)
R-Value Work: 0.152 (Depositor), 0.169 (DCC)
R-Value Observed: 0.153 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.679	α = 90
b = 106.187	β = 90.95
c = 88.205	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
HKL-3000	phasing
MLPHARE	phasing
DM	model building
SHELXD	phasing
ARP/wARP	model building
CCP4	model building
REFMAC	refinement
HKL-2000	data scaling
DM	phasing
CCP4	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-04-07

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2010-04-07
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-11-08
Changes: Advisory, Refinement description
Version 1.3: 2024-11-27
Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary

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Help and Resources

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Structure of 4-hydroxy-2-oxoglutarate aldolase from bacillus cereus at 1.45 a resolution.

Structure of 4-Hydroxy-2-Oxoglutarate Aldolase from Bacillus Cereus at 1.45 A Resolution.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)

3M6Y | pdb_00003m6y