2RIR | pdb_00002rir

Crystal structure of dipicolinate synthase, A chain, from Bacillus subtilis

PDB DOI: https://doi.org/10.2210/pdb2RIR/pdb

Classification: OXIDOREDUCTASE
Organism(s): Bacillus subtilis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2007-10-12 Released: 2007-10-23
Deposition Author(s): Osipiuk, J., Quartey, P., Moy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.79 Å
R-Value Free:
0.249 (Depositor), 0.242 (DCC)
R-Value Work:
0.199 (Depositor), 0.193 (DCC)
R-Value Observed:
0.201 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of dipicolinate synthase, A chain, from Bacillus subtilis.

Osipiuk, J., Quartey, P., Moy, S., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 266.36 kDa
Atom Count: 18,495
Modeled Residue Count: 2,376
Deposited Residue Count: 2,400
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipicolinate synthase, A chain	A, B, C, D, E A, B, C, D, E, F, G, H	300	Bacillus subtilis	Mutation(s): 0 Gene Names: spoVFA, dpaA, BSU16730 EC: 1.3.1
UniProt
Find proteins for Q04809 (Bacillus subtilis (strain 168)) Explore Q04809 Go to UniProtKB: Q04809
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q04809
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download Ideal Coordinates CCD File SDF format, chain W [auth H] SDF format, chain T [auth G] SDF format, chain R [auth F] SDF format, chain Q [auth E] SDF format, chain O [auth D] SDF format, chain M [auth C] SDF format, chain L [auth B] SDF format, chain J [auth A] MOL2 format, chain W [auth H] MOL2 format, chain T [auth G] MOL2 format, chain R [auth F] MOL2 format, chain Q [auth E] MOL2 format, chain O [auth D] MOL2 format, chain M [auth C] MOL2 format, chain L [auth B] MOL2 format, chain J [auth A] mmCIF format, chain W [auth H] mmCIF format, chain T [auth G] mmCIF format, chain R [auth F] mmCIF format, chain Q [auth E] mmCIF format, chain O [auth D] mmCIF format, chain M [auth C] mmCIF format, chain L [auth B] mmCIF format, chain J [auth A]	J [auth A] L [auth B] M [auth C] O [auth D] Q [auth E] J [auth A], L [auth B], M [auth C], O [auth D], Q [auth E], R [auth F], T [auth G], W [auth H]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain Q [auth E] Focus chain R [auth F] Focus chain T [auth G] Focus chain W [auth H] Interactions & Density Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain Q [auth E] Focus chain R [auth F] Focus chain T [auth G] Focus chain W [auth H]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain V [auth H] SDF format, chain U [auth H] SDF format, chain S [auth G] SDF format, chain P [auth E] SDF format, chain N [auth D] SDF format, chain K [auth B] SDF format, chain I [auth A] MOL2 format, chain V [auth H] MOL2 format, chain U [auth H] MOL2 format, chain S [auth G] MOL2 format, chain P [auth E] MOL2 format, chain N [auth D] MOL2 format, chain K [auth B] MOL2 format, chain I [auth A] mmCIF format, chain V [auth H] mmCIF format, chain U [auth H] mmCIF format, chain S [auth G] mmCIF format, chain P [auth E] mmCIF format, chain N [auth D] mmCIF format, chain K [auth B] mmCIF format, chain I [auth A]	I [auth A] K [auth B] N [auth D] P [auth E] S [auth G] I [auth A], K [auth B], N [auth D], P [auth E], S [auth G], U [auth H], V [auth H]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Focus chain K [auth B] Focus chain N [auth D] Focus chain P [auth E] Focus chain S [auth G] Focus chain U [auth H] Focus chain V [auth H] Interactions & Density Focus chain I [auth A] Focus chain K [auth B] Focus chain N [auth D] Focus chain P [auth E] Focus chain S [auth G] Focus chain U [auth H] Focus chain V [auth H]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.79 Å
R-Value Free: 0.249 (Depositor), 0.242 (DCC)
R-Value Work: 0.199 (Depositor), 0.193 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 261.578	α = 90
b = 75.108	β = 119.74
c = 200.464	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-2000	data reduction
SHELXD	phasing
SOLVE	phasing
RESOLVE	phasing
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2007-10-23

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2007-10-23
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary

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Crystal structure of dipicolinate synthase, A chain, from Bacillus subtilis

Crystal structure of dipicolinate synthase, A chain, from Bacillus subtilis.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations