3P6K | pdb_00003p6k

Crystal structure of a PLP-dependent aminotransferase (ZP_03625122.1) from Streptococcus suis 89-1591 at 2.07 A resolution

PDB DOI: https://doi.org/10.2210/pdb3P6K/pdb

Classification: TRANSFERASE
Organism(s): Streptococcus suis 89/1591
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-10-11 Released: 2010-10-27
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.07 Å
R-Value Free:
0.208 (Depositor), 0.213 (DCC)
R-Value Work:
0.178 (Depositor), 0.184 (DCC)
R-Value Observed:
0.180 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3P6K

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

Literature

Crystal structure of a PLP-dependent aminotransferase (ZP_03625122.1) from Streptococcus suis 89-1591 at 2.07 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 86.43 kDa
Atom Count: 6,384
Modeled Residue Count: 743
Deposited Residue Count: 750
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminotransferase class I and II	A, B	375	Streptococcus suis 89/1591	Mutation(s): 0 Gene Names: SsuiDRAFT_2941

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain C [auth A] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain C [auth A] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain C [auth A]	C [auth A], G [auth B], H [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B] Focus chain H [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
UNL Query on UNL Download:Ideal Coordinates CCD File	E [auth B], F [auth B]	Unknown ligand LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Focus chain F [auth B] Interactions & Density Focus chain E [auth B] Focus chain F [auth B]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP Query on LLP	A, B	L-PEPTIDE LINKING	C₁₄ H₂₂ N₃ O₇ P		LYS
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.07 Å
R-Value Free: 0.208 (Depositor), 0.213 (DCC)
R-Value Work: 0.178 (Depositor), 0.184 (DCC)
R-Value Observed: 0.180 (Depositor)

Diffraction Data:

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.979	α = 90
b = 83.979	β = 90
c = 176.391	γ = 120

Software Package:

Software Name	Purpose
SHELX	phasing
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-10-27

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2010-10-27
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2011-07-20
Changes: Structure summary
Version 1.3: 2023-02-01
Changes: Database references, Derived calculations

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.