3TY1 | pdb_00003ty1

Crystal structure of a putative aldose 1-epimerase (KPN_04629) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 1.90 A resolution

PDB DOI: https://doi.org/10.2210/pdb3TY1/pdb

Classification: ISOMERASE
Organism(s): Klebsiella pneumoniae subsp. pneumoniae MGH 78578
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-09-23 Released: 2011-12-28
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.193 (Depositor), 0.199 (DCC)
R-Value Work:
0.158 (Depositor), 0.167 (DCC)
R-Value Observed:
0.160 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of a Hypothetical aldose 1-epimerase (KPN_04629) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 1.90 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 130.8 kDa
Atom Count: 10,002
Modeled Residue Count: 1,152
Deposited Residue Count: 1,152
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical aldose 1-epimerase	A, B, C	384	Klebsiella pneumoniae subsp. pneumoniae MGH 78578	Mutation(s): 0 Gene Names: trxC, KPN78578_45560, KPN_04629
UniProt
Find proteins for A6THE6 (Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)) Explore A6THE6 Go to UniProtKB: A6THE6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A6THE6
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 W [auth B] SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain BA [auth C] SDF format, chain AA [auth C] MOL2 format, chain W [auth B] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain BA [auth C] MOL2 format, chain AA [auth C] mmCIF format, chain W [auth B] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain BA [auth C] mmCIF format, chain AA [auth C]	AA [auth C] BA [auth C] M [auth A] N [auth A] S [auth B] AA [auth C], BA [auth C], M [auth A], N [auth A], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain M [auth A] Focus chain N [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain M [auth A] Focus chain N [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B]
MRD Query on MRD Download:Ideal Coordinates CCD File SDF format, chain CA [auth C] MOL2 format, chain CA [auth C] mmCIF format, chain CA [auth C]	CA [auth C]	(4R)-2-METHYLPENTANE-2,4-DIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-RXMQYKEDSA-N		Interactions Focus chain CA [auth C] Interactions & Density Focus chain CA [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain Y [auth C] SDF format, chain R [auth B] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain Z [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain R [auth B] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain Z [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain R [auth B] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] I [auth A] J [auth A] K [auth A] G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], R [auth B], Y [auth C], Z [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain R [auth B] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain R [auth B] Focus chain Y [auth C] Focus chain Z [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain X [auth C] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain X [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain X [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth A] O [auth B] P [auth B] D [auth A], E [auth A], F [auth A], O [auth B], P [auth B], Q [auth B], X [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain X [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain X [auth C]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.193 (Depositor), 0.199 (DCC)
R-Value Work: 0.158 (Depositor), 0.167 (DCC)
R-Value Observed: 0.160 (Depositor)

Diffraction Data:

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.033	α = 90
b = 119.953	β = 106.72
c = 103.015	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
SCALA	data scaling
REFMAC	refinement
MOSFLM	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2011-12-28

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2011-12-28
Type: Initial release
Version 1.1: 2014-12-24
Changes: Structure summary
Version 1.2: 2017-10-25
Changes: Author supporting evidence, Refinement description
Version 1.3: 2023-02-01
Changes: Database references, Derived calculations
Version 1.4: 2024-10-16
Changes: Data collection, Structure summary