4RDV | pdb_00004rdv

The structure of N-formimino-L-Glutamate Iminohydrolase from Pseudomonas aeruginosa complexed with N-formimino-L-Aspartate

PDB DOI: https://doi.org/10.2210/pdb4RDV/pdb

Classification: HYDROLASE
Organism(s): Pseudomonas aeruginosa PAO1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-09-19 Released: 2014-10-08
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Marti-Arbona, R., Raushel, F.M., Almo, S.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.08 Å
R-Value Free:
0.183 (Depositor), 0.184 (DCC)
R-Value Work:
0.144 (Depositor), 0.146 (DCC)
R-Value Observed:
0.146 (Depositor)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

The structure of N-formimino-L-Glutamate Iminohydrolase from Pseudomonas aeruginosa complexed with N-formimino-L-Aspartate

Fedorov, A.A., Fedorov, E.V., Marti-Arbona, R., Raushel, F.M., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 198.86 kDa
Atom Count: 15,031
Modeled Residue Count: 1,803
Deposited Residue Count: 1,812
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-FORMIMINO-L-GLUTAMATE IMINOHYDROLASE	A, B, C, D	453	Pseudomonas aeruginosa PAO1	Mutation(s): 0 Gene Names: PA5106 EC: 3.5.3.13
UniProt
Find proteins for Q9HU77 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HU77 Go to UniProtKB: Q9HU77
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9HU77
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NFQ Query on NFQ Download:Ideal Coordinates CCD File SDF format, chain N [auth D] SDF format, chain I [auth C] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain N [auth D] MOL2 format, chain I [auth C] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain N [auth D] mmCIF format, chain I [auth C] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], I [auth C], N [auth D]	N-[(E)-iminomethyl]-L-aspartic acid C₅ H₈ N₂ O₄ XTPIFIMCFHNJOH-VKHMYHEASA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain N [auth D]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain P [auth D] MOL2 format, chain P [auth D] mmCIF format, chain P [auth D]	P [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain P [auth D] Interactions & Density Focus chain P [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain K [auth C] MOL2 format, chain L [auth C] MOL2 format, chain K [auth C] mmCIF format, chain L [auth C] mmCIF format, chain K [auth C]	K [auth C], L [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth C] Focus chain L [auth C] Interactions & Density Focus chain K [auth C] Focus chain L [auth C]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain O [auth D] SDF format, chain J [auth C] SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain O [auth D] MOL2 format, chain J [auth C] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain O [auth D] mmCIF format, chain J [auth C] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B], J [auth C], O [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain O [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain O [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain M [auth C] MOL2 format, chain M [auth C] mmCIF format, chain M [auth C]	M [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain M [auth C] Interactions & Density Focus chain M [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.08 Å
R-Value Free: 0.183 (Depositor), 0.184 (DCC)
R-Value Work: 0.144 (Depositor), 0.146 (DCC)
R-Value Observed: 0.146 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 304.047	α = 90
b = 67.248	β = 91.5
c = 98.231	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
BALBES	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-10-08

Deposition Author(s):

Marti-Arbona, R.

Revision History (Full details and data files)

Version 1.0: 2014-10-08
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, 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.