6BLG | pdb_00006blg

Crystal Structure of Sugar Transaminase from Klebsiella pneumoniae Complexed with PLP

PDB DOI: https://doi.org/10.2210/pdb6BLG/pdb

Classification: TRANSFERASE
Organism(s): Klebsiella pneumoniae subsp. pneumoniae MGH 78578
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-11-10 Released: 2017-11-22
Deposition Author(s): Maltseva, N., Kim, Y., Shatsman, S., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
Funding Organization(s): National Institutes of Health

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.225 (Depositor), 0.227 (DCC)
R-Value Work:
0.175 (Depositor), 0.178 (DCC)
R-Value Observed:
0.177 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of Sugar Transaminase from Klebsiella pneumoniae Complexed with PLP

Maltseva, N., Kim, Y., Shatsman, S., Satchell, K.J.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 43.79 kDa
Atom Count: 3,127
Modeled Residue Count: 376
Deposited Residue Count: 379
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
dTDP-4-amino-4,6-dideoxygalactose transaminase	A	379	Klebsiella pneumoniae subsp. pneumoniae MGH 78578	Mutation(s): 0 Gene Names: wecE, KPN_04291 EC: 2.6.1.59
UniProt
Find proteins for A6TGH9 (Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)) Explore A6TGH9 Go to UniProtKB: A6TGH9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A6TGH9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain N [auth A] MOL2 format, chain N [auth A] mmCIF format, chain N [auth A]	N [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Interactions & Density Focus chain N [auth A]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A]	L [auth A], M [auth A]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain L [auth A] Focus chain M [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] MOL2 format, chain C [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] mmCIF format, chain C [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A]	C [auth A], J [auth A], K [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain C [auth A] Focus chain J [auth A] Focus chain K [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP Query on LLP	A	L-PEPTIDE LINKING	C₁₄ H₂₂ N₃ O₇ P		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.225 (Depositor), 0.227 (DCC)
R-Value Work: 0.175 (Depositor), 0.178 (DCC)
R-Value Observed: 0.177 (Depositor)

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.853	α = 90
b = 130.853	β = 90
c = 138.752	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2017-11-22

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Funding Organization	Location	Grant Number
National Institutes of Health	United States	--

Revision History (Full details and data files)

Version 1.0: 2017-11-22
Type: Initial release
Version 1.1: 2017-12-06
Changes: Author supporting evidence
Version 1.2: 2023-10-04
Changes: Data collection, Database references, Refinement description
Version 1.3: 2023-11-15
Changes: Data collection