4H73 | pdb_00004h73

Thermostable aldehyde dehydrogenase from Pyrobaculum sp. complexed with NADP+

PDB DOI: https://doi.org/10.2210/pdb4H73/pdb

Classification: OXIDOREDUCTASE
Organism(s): Pyrobaculum ferrireducens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-09-20 Released: 2013-10-02
Deposition Author(s): Petrova, T., Shabalin, I.G., Bezsudnova, E.Y., Boyko, K.M., Mardanov, A.V., Gumerov, V.M., Ravin, N.V., Popov, V.O.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.261 (Depositor), 0.250 (DCC)
R-Value Work:
0.212 (Depositor), 0.210 (DCC)
R-Value Observed:
0.215 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Thermostable aldehyde dehydrogenase from Pyrobaculum sp. complexed with NADP+

Petrova, T., Shabalin, I.G., Bezsudnova, E.Y., Boyko, K.M., Mardanov, A.V., M Gumerov, V., Ravin, N.V., Popov, V.O.

To be published.

Macromolecule Content

Total Structure Weight: 441.87 kDa
Atom Count: 31,843
Modeled Residue Count: 3,872
Deposited Residue Count: 3,928
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aldehyde dehydrogenase	A, B, C, D, E A, B, C, D, E, F, G, H	491	Pyrobaculum ferrireducens	Mutation(s): 0 Gene Names: P186_1147
UniProt
Find proteins for G7VCG0 (Pyrobaculum ferrireducens) Explore G7VCG0 Go to UniProtKB: G7VCG0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	G7VCG0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NDP Query on NDP Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain L [auth C] SDF format, chain N [auth D] SDF format, chain O [auth E] SDF format, chain Q [auth F] SDF format, chain R [auth G] SDF format, chain T [auth H] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth C] MOL2 format, chain N [auth D] MOL2 format, chain O [auth E] MOL2 format, chain Q [auth F] MOL2 format, chain R [auth G] MOL2 format, chain T [auth H] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth C] mmCIF format, chain N [auth D] mmCIF format, chain O [auth E] mmCIF format, chain Q [auth F] mmCIF format, chain R [auth G] mmCIF format, chain T [auth H]	I [auth A] K [auth B] L [auth C] N [auth D] O [auth E] I [auth A], K [auth B], L [auth C], N [auth D], O [auth E], Q [auth F], R [auth G], T [auth H]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Interactions Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain O [auth E] Focus chain Q [auth F] Focus chain R [auth G] Focus chain T [auth H] Interactions & Density Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain O [auth E] Focus chain Q [auth F] Focus chain R [auth G] Focus chain T [auth H]
NI Query on NI Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain M [auth C] SDF format, chain P [auth E] SDF format, chain S [auth G] MOL2 format, chain J [auth A] MOL2 format, chain M [auth C] MOL2 format, chain P [auth E] MOL2 format, chain S [auth G] mmCIF format, chain J [auth A] mmCIF format, chain M [auth C] mmCIF format, chain P [auth E] mmCIF format, chain S [auth G]	J [auth A], M [auth C], P [auth E], S [auth G]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain M [auth C] Focus chain P [auth E] Focus chain S [auth G] Interactions & Density Focus chain J [auth A] Focus chain M [auth C] Focus chain P [auth E] Focus chain S [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.261 (Depositor), 0.250 (DCC)
R-Value Work: 0.212 (Depositor), 0.210 (DCC)
R-Value Observed: 0.215 (Depositor)

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 164.21	α = 90
b = 183.77	β = 90
c = 206.47	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-10-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-10-02
Type: Initial release
Version 1.1: 2018-01-24
Changes: Structure summary
Version 1.2: 2024-02-28
Changes: Data collection, Database references, Derived calculations

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Help and Resources

.id_divider{ color: #ccc; padding: 0 10px 0 10px; } .extended_id_info{ color: #ccc; font-size: 18px; position: relative; top: -10px; left: 4px; } 4H73 | pdb_00004h73

Thermostable aldehyde dehydrogenase from Pyrobaculum sp. complexed with NADP+

Thermostable aldehyde dehydrogenase from Pyrobaculum sp. complexed with NADP+

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)

4H73 | pdb_00004h73