4GO4 | pdb_00004go4

Crystal structure of PnpE in complex with Nicotinamide adenine dinucleotide

PDB DOI: https://doi.org/10.2210/pdb4GO4/pdb

Classification: OXIDOREDUCTASE
Organism(s): Pseudomonas sp. WBC-3
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2012-08-18 Released: 2013-09-04
Deposition Author(s): Su, J., Zhang, C., Liu, S., Zhu, D., Gu, L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free:
0.251 (Depositor), 0.240 (DCC)
R-Value Work:
0.207 (Depositor), 0.200 (DCC)
R-Value Observed:
0.208 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of PnpE in complex with Nicotinamide adenine dinucleotide

Su, J., Zhang, C., Liu, S., Zhu, D., Gu, L.

To be published.

Macromolecule Content

Total Structure Weight: 432.68 kDa
Atom Count: 30,071
Modeled Residue Count: 3,896
Deposited Residue Count: 3,960
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative gamma-hydroxymuconic semialdehyde dehydrogenase	A, B, C, D, E A, B, C, D, E, F, G, H	495	Pseudomonas sp. WBC-3	Mutation(s): 2 Gene Names: pnpE EC: 1.2.1.3
UniProt
Find proteins for C1I208 (Pseudomonas sp. (strain WBC-3)) Explore C1I208 Go to UniProtKB: C1I208
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C1I208
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain P [auth H] SDF format, chain O [auth G] SDF format, chain N [auth F] SDF format, chain M [auth E] SDF format, chain L [auth D] SDF format, chain K [auth C] SDF format, chain J [auth B] SDF format, chain I [auth A] MOL2 format, chain P [auth H] MOL2 format, chain O [auth G] MOL2 format, chain N [auth F] MOL2 format, chain M [auth E] MOL2 format, chain L [auth D] MOL2 format, chain K [auth C] MOL2 format, chain J [auth B] MOL2 format, chain I [auth A] mmCIF format, chain P [auth H] mmCIF format, chain O [auth G] mmCIF format, chain N [auth F] mmCIF format, chain M [auth E] mmCIF format, chain L [auth D] mmCIF format, chain K [auth C] mmCIF format, chain J [auth B] mmCIF format, chain I [auth A]	I [auth A] J [auth B] K [auth C] L [auth D] M [auth E] I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth F] Focus chain O [auth G] Focus chain P [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth F] Focus chain O [auth G] Focus chain P [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.251 (Depositor), 0.240 (DCC)
R-Value Work: 0.207 (Depositor), 0.200 (DCC)
R-Value Observed: 0.208 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.911	α = 90
b = 154.539	β = 95.24
c = 143.435	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-09-04

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-09-04
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description

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Crystal structure of PnpE in complex with Nicotinamide adenine dinucleotide

Crystal structure of PnpE in complex with Nicotinamide adenine dinucleotide

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)

4GO4 | pdb_00004go4