3M5V | pdb_00003m5v

Crystal Structure of Dihydrodipicolinate Synthase from Campylobacter jejuni

PDB DOI: https://doi.org/10.2210/pdb3M5V/pdb

Classification: LYASE
Organism(s): Campylobacter jejuni
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2010-03-13 Released: 2010-04-28
Deposition Author(s): Kim, Y., Zhou, M., Kwon, K., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.181 (Depositor), 0.182 (DCC)
R-Value Work:
0.146 (Depositor), 0.148 (DCC)
R-Value Observed:
0.148 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of Dihydrodipicolinate Synthase from Campylobacter jejuni

Kim, Y., Zhou, M., Kwon, K., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 134.83 kDa
Atom Count: 10,641
Modeled Residue Count: 1,192
Deposited Residue Count: 1,204
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrodipicolinate synthase	A, B, C, D	301	Campylobacter jejuni	Mutation(s): 0 Gene Names: Cj0806, dapA EC: 4.2.1.52 (PDB Primary Data), 4.3.3.7 (UniProt)
UniProt
Find proteins for Q9PPB4 (Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168)) Explore Q9PPB4 Go to UniProtKB: Q9PPB4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9PPB4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain M [auth B] SDF format, chain T [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain M [auth B] MOL2 format, chain T [auth C] mmCIF format, chain AA [auth D] mmCIF format, chain M [auth B] mmCIF format, chain T [auth C]	AA [auth D], M [auth B], T [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain M [auth B] Focus chain T [auth C] Interactions & Density Focus chain AA [auth D] Focus chain M [auth B] Focus chain T [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain J [auth B] SDF format, chain S [auth C] SDF format, chain U [auth D] SDF format, chain V [auth D] SDF format, chain Z [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain S [auth C] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] MOL2 format, chain Z [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth B] mmCIF format, chain S [auth C] mmCIF format, chain U [auth D] mmCIF format, chain V [auth D] mmCIF format, chain Z [auth D]	E [auth A] F [auth A] G [auth A] I [auth A] J [auth B] E [auth A], F [auth A], G [auth A], I [auth A], J [auth B], S [auth C], U [auth D], V [auth D], Z [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain S [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain Z [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain S [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain Z [auth D]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain O [auth B] MOL2 format, chain O [auth B] mmCIF format, chain O [auth B]	O [auth B]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain O [auth B] Interactions & Density Focus chain O [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain N [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain Y [auth D] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain N [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D] mmCIF format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain N [auth B] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D] mmCIF format, chain Y [auth D]	H [auth A] K [auth B] L [auth B] N [auth B] P [auth C] H [auth A], K [auth B], L [auth B], N [auth B], P [auth C], Q [auth C], R [auth C], W [auth D], X [auth D], Y [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Interactions & Density Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [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: 1.80 Å
R-Value Free: 0.181 (Depositor), 0.182 (DCC)
R-Value Work: 0.146 (Depositor), 0.148 (DCC)
R-Value Observed: 0.148 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.36	α = 90
b = 86.032	β = 90
c = 198.948	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
SHELXS	phasing
MLPHARE	phasing
RESOLVE	model building
SOLVE	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
RESOLVE	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-04-28

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2010-04-28
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2012-02-29
Changes: Database references, Structure summary
Version 1.3: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary