4H4W | pdb_00004h4w

Crystal Structure of Ferredoxin reductase, BphA4 E175C/T176R/Q177G mutant (reduced form)

PDB DOI: https://doi.org/10.2210/pdb4H4W/pdb

Classification: OXIDOREDUCTASE
Organism(s): Acidovorax sp. KKS102
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2012-09-18 Released: 2013-10-09
Deposition Author(s): Nishizawa, A., Harada, A., Senda, M., Tachihara, Y., Muramatsu, D., Kishigami, S., Mori, S., Sugiyama, K., Senda, T., Kimura, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.216 (Depositor), 0.226 (DCC)
R-Value Work:
0.199 (Depositor)
R-Value Observed:
0.200 (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

Random Mutagenesis with the Project Assessment for Complete Conversion of Co-Factor Specificity of a Ferredoxin Reductase BphA4

Nishizawa, A., Harada, A., Senda, M., Tachihara, Y., Muramatsu, D., Kishigami, S., Mori, S., Sugiyama, K., Senda, T., Kimura, S.

To be published.

Macromolecule Content

Total Structure Weight: 44.94 kDa
Atom Count: 3,279
Modeled Residue Count: 399
Deposited Residue Count: 408
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Biphenyl dioxygenase ferredoxin reductase subunit	A	408	Acidovorax sp. KKS102	Mutation(s): 3 Gene Names: bphA4 EC: 1.18.1.3
UniProt
Find proteins for A0ACD6B9C0 (Acidovorax sp. KKS102) Explore A0ACD6B9C0 Go to UniProtKB: A0ACD6B9C0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ACD6B9C0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
NAP Query on NAP Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.216 (Depositor), 0.226 (DCC)
R-Value Work: 0.199 (Depositor)
R-Value Observed: 0.200 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.023	α = 90
b = 98.023	β = 90
c = 171.088	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
MOLREP	phasing
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-10-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-10-09
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description

4H4W | pdb_00004h4w

Crystal Structure of Ferredoxin reductase, BphA4 E175C/T176R/Q177G mutant (reduced form)

Literature

Random Mutagenesis with the Project Assessment for Complete Conversion of Co-Factor Specificity of a Ferredoxin Reductase BphA4

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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