4XG1 | pdb_00004xg1

Psychromonas ingrahamii diaminopimelate decarboxylase with LLP

PDB DOI: https://doi.org/10.2210/pdb4XG1/pdb

Classification: LYASE
Organism(s): Psychromonas ingrahamii 37
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-12-30 Released: 2016-03-09
Deposition Author(s): Peverelli, M.G., Wubben, J.M., Panjikar, S., Perugini, M.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.246 (Depositor), 0.250 (DCC)
R-Value Work:
0.211 (Depositor), 0.215 (DCC)
R-Value Observed:
0.212 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Expression to crystallization of diaminopimelate decarboxylase from the psychrophile Psychromonas ingrahamii

Peverelli, M.G., Newman, J., Panjikar, S., Perugini, M.A.

To be published.

Macromolecule Content

Total Structure Weight: 191.8 kDa
Atom Count: 13,006
Modeled Residue Count: 1,625
Deposited Residue Count: 1,708
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diaminopimelate decarboxylase	A, B, C, D	427	Psychromonas ingrahamii 37	Mutation(s): 0 Gene Names: lysA, Ping_0041 EC: 4.1.1.20
UniProt
Find proteins for A1SR00 (Psychromonas ingrahamii (strain DSM 17664 / CCUG 51855 / 37)) Explore A1SR00 Go to UniProtKB: A1SR00
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A1SR00
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LLP Query on LLP Download:Ideal Coordinates CCD File SDF format, chain X [auth C] SDF format, chain T [auth B] SDF format, chain L [auth A] SDF format, chain BA [auth D] MOL2 format, chain X [auth C] MOL2 format, chain T [auth B] MOL2 format, chain L [auth A] MOL2 format, chain BA [auth D] mmCIF format, chain X [auth C] mmCIF format, chain T [auth B] mmCIF format, chain L [auth A] mmCIF format, chain BA [auth D]	BA [auth D], L [auth A], T [auth B], X [auth C]	(2S)-2-amino-6-[[3-hydroxy-2-methyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]hexanoic acid C₁₄ H₂₂ N₃ O₇ P YQSOQJORMNSDJL-QFULYMJESA-N		Interactions Focus chain BA [auth D] Focus chain L [auth A] Focus chain T [auth B] Focus chain X [auth C] Interactions & Density Focus chain BA [auth D] Focus chain L [auth A] Focus chain T [auth B] Focus chain X [auth C]
SCN Query on SCN Download:Ideal Coordinates CCD File SDF format, chain Y [auth D] SDF format, chain V [auth C] SDF format, chain U [auth C] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain Y [auth D] MOL2 format, chain V [auth C] MOL2 format, chain U [auth C] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain Y [auth D] mmCIF format, chain V [auth C] mmCIF format, chain U [auth C] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] M [auth B] E [auth A], F [auth A], G [auth A], H [auth A], M [auth B], N [auth B], U [auth C], V [auth C], Y [auth D]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain Y [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain Y [auth D]
TME Query on TME Download:Ideal Coordinates CCD File SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain K [auth A] SDF format, chain AA [auth D] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain K [auth A] MOL2 format, chain AA [auth D] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain K [auth A] mmCIF format, chain AA [auth D]	AA [auth D], K [auth A], Q [auth B], R [auth B], S [auth B]	PROPANE C₃ H₈ ATUOYWHBWRKTHZ-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain K [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain AA [auth D] Focus chain K [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain W [auth C] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] MOL2 format, chain Z [auth D] MOL2 format, chain W [auth C] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] mmCIF format, chain Z [auth D] mmCIF format, chain W [auth C] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A]	I [auth A] J [auth A] O [auth B] P [auth B] W [auth C] I [auth A], J [auth A], O [auth B], P [auth B], W [auth C], Z [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain W [auth C] Focus chain Z [auth D] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain W [auth C] Focus chain Z [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.246 (Depositor), 0.250 (DCC)
R-Value Work: 0.211 (Depositor), 0.215 (DCC)
R-Value Observed: 0.212 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.96	α = 90
b = 103.13	β = 94.77
c = 93.59	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
MOSFLM	data reduction
SCALA	data scaling
SHELX	phasing
REFMAC	refinement
Coot	model building
XDS	data reduction
Auto-Rickshaw	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-03-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-03-09
Type: Initial release
Version 1.1: 2017-09-27
Changes: Author supporting evidence, Data collection, Derived calculations
Version 1.2: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2023-11-15
Changes: Data collection