3QN3 | pdb_00003qn3

Phosphopyruvate hydratase from Campylobacter jejuni.

PDB DOI: https://doi.org/10.2210/pdb3QN3/pdb

Classification: LYASE
Organism(s): Campylobacter jejuni
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-02-07 Released: 2011-02-23
Deposition Author(s): Osipiuk, J., Gu, M., Kwon, K., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.13 Å
R-Value Free:
0.216 (Depositor), 0.220 (DCC)
R-Value Work:
0.176 (Depositor), 0.180 (DCC)
R-Value Observed:
0.178 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Phosphopyruvate hydratase from Campylobacter jejuni.

Osipiuk, J., Gu, M., Kwon, K., Anderson, W.F., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 182.16 kDa
Atom Count: 13,827
Modeled Residue Count: 1,660
Deposited Residue Count: 1,668
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Enolase	A, B, C, D	417	Campylobacter jejuni	Mutation(s): 0 Gene Names: Cj1672c, eno EC: 4.2.1.11
UniProt
Find proteins for P42448 (Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168)) Explore P42448 Go to UniProtKB: P42448
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P42448
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain Q [auth D] SDF format, chain L [auth C] SDF format, chain I [auth B] SDF format, chain F [auth A] MOL2 format, chain Q [auth D] MOL2 format, chain L [auth C] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] mmCIF format, chain Q [auth D] mmCIF format, chain L [auth C] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A]	F [auth A], I [auth B], L [auth C], Q [auth D]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain Q [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain Q [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain R [auth D] SDF format, chain O [auth C] SDF format, chain J [auth B] MOL2 format, chain R [auth D] MOL2 format, chain O [auth C] MOL2 format, chain J [auth B] mmCIF format, chain R [auth D] mmCIF format, chain O [auth C] mmCIF format, chain J [auth B]	J [auth B], O [auth C], R [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain J [auth B] Focus chain O [auth C] Focus chain R [auth D] Interactions & Density Focus chain J [auth B] Focus chain O [auth C] Focus chain R [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain M [auth C] SDF format, chain G [auth A] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] MOL2 format, chain G [auth A] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C] mmCIF format, chain G [auth A]	G [auth A], M [auth C], N [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain M [auth C] Focus chain N [auth C] Interactions & Density Focus chain G [auth A] Focus chain M [auth C] Focus chain N [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain P [auth D] SDF format, chain K [auth C] SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain P [auth D] MOL2 format, chain K [auth C] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain P [auth D] mmCIF format, chain K [auth C] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], H [auth B], K [auth C], P [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain P [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain P [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.13 Å
R-Value Free: 0.216 (Depositor), 0.220 (DCC)
R-Value Work: 0.176 (Depositor), 0.180 (DCC)
R-Value Observed: 0.178 (Depositor)

Diffraction Data: https://doi.org/10.18430/m33qn3

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.47	α = 90
b = 148.886	β = 90
c = 234.719	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing
HKL-3000	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-02-23

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2011-02-23
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description