3LY1 | pdb_00003ly1

Crystal structure of Putative histidinol-phosphate aminotransferase (YP_050345.1) from Erwinia carotovora atroseptica SCRI1043 at 1.80 A resolution

PDB DOI: https://doi.org/10.2210/pdb3LY1/pdb

Classification: TRANSFERASE
Organism(s): Pectobacterium atrosepticum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-02-25 Released: 2010-03-31
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.206 (Depositor), 0.221 (DCC)
R-Value Work:
0.176 (Depositor), 0.195 (DCC)
R-Value Observed:
0.178 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of Putative histidinol-phosphate aminotransferase (YP_050345.1) from Erwinia carotovora atroseptica SCRI1043 at 1.80 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 160.12 kDa
Atom Count: 13,056
Modeled Residue Count: 1,393
Deposited Residue Count: 1,416
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative histidinol-phosphate aminotransferase	A, B, C, D	354	Pectobacterium atrosepticum	Mutation(s): 0 Gene Names: ECA2250
UniProt
Find proteins for Q6D4Z0 (Pectobacterium atrosepticum (strain SCRI 1043 / ATCC BAA-672)) Explore Q6D4Z0 Go to UniProtKB: Q6D4Z0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6D4Z0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP Query on PLP Download:Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain E [auth A] SDF format, chain M [auth B] SDF format, chain R [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain E [auth A] MOL2 format, chain M [auth B] MOL2 format, chain R [auth C] mmCIF format, chain BA [auth D] mmCIF format, chain E [auth A] mmCIF format, chain M [auth B] mmCIF format, chain R [auth C]	BA [auth D], E [auth A], M [auth B], R [auth C]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain E [auth A] Focus chain M [auth B] Focus chain R [auth C] Interactions & Density Focus chain BA [auth D] Focus chain E [auth A] Focus chain M [auth B] Focus chain R [auth C]
CIT Query on CIT Download:Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain F [auth A] SDF format, chain S [auth C] SDF format, chain N [auth B] MOL2 format, chain CA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain S [auth C] MOL2 format, chain N [auth B] mmCIF format, chain CA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain S [auth C] mmCIF format, chain N [auth B]	CA [auth D], F [auth A], N [auth B], S [auth C]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain F [auth A] Focus chain N [auth B] Focus chain S [auth C] Interactions & Density Focus chain CA [auth D] Focus chain F [auth A] Focus chain N [auth B] Focus chain S [auth C]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain FA [auth D] SDF format, chain HA [auth D] SDF format, chain I [auth A] SDF format, chain IA [auth D] SDF format, chain L [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain Z [auth C] SDF format, chain Y [auth C] SDF format, chain Q [auth B] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain H [auth A] SDF format, chain GA [auth D] SDF format, chain G [auth A] MOL2 format, chain AA [auth C] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain HA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain H [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain G [auth A] mmCIF format, chain AA [auth C] mmCIF format, chain DA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain HA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain L [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C] mmCIF format, chain Z [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain H [auth A] mmCIF format, chain GA [auth D] mmCIF format, chain G [auth A]	AA [auth C] DA [auth D] EA [auth D] FA [auth D] G [auth A] AA [auth C], DA [auth D], EA [auth D], FA [auth D], G [auth A], GA [auth D], H [auth A], HA [auth D], I [auth A], IA [auth D], J [auth A], K [auth A], L [auth A], O [auth B], P [auth B], Q [auth B], T [auth C], U [auth C], V [auth C], W [auth C], X [auth C], Y [auth C], Z [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]

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: 0.206 (Depositor), 0.221 (DCC)
R-Value Work: 0.176 (Depositor), 0.195 (DCC)
R-Value Observed: 0.178 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.625	α = 90
b = 150.477	β = 94.38
c = 100.092	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
MolProbity	model building

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-03-31

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2010-03-31
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2019-07-17
Changes: Data collection, Derived calculations, Refinement description
Version 1.4: 2023-02-01
Changes: Database references, Derived calculations