2EIX

The Structure of Physarum polycephalum cytochrome b5 reductase

PDB DOI: https://doi.org/10.2210/pdb2EIX/pdb

Classification: OXIDOREDUCTASE
Organism(s): Physarum polycephalum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-03-14 Released: 2007-04-17
Deposition Author(s): Kim, S.W., Suga, M., Ogasahara, K., Ikegami, T., Minami, Y., Yubisui, T., Tsukihara, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.56 Å
R-Value Free:
0.226 (Depositor), 0.220 (DCC)
R-Value Work:
0.180 (Depositor), 0.190 (DCC)

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

Structure of Physarum polycephalum cytochrome b5 reductase at 1.56 A resolution.

Kim, S., Suga, M., Ogasahara, K., Ikegami, T., Minami, Y., Yubisui, T., Tsukihara, T.

(2007) Acta Crystallogr Sect F Struct Biol Cryst Commun 63: 274-279

PubMed: 17401193 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1107/S1744309107010731
Primary Citation of Related Structures:
2EIX

PubMed Abstract:
Physarum polycephalum cytochrome b(5) reductase catalyzes the reduction of cytochrome b(5) by NADH. The structure of P. polycephalum cytochrome b(5) reductase was determined at a resolution of 1.56 A. The molecular structure was compared with that of human cytochrome b(5) reductase, which had previously been determined at 1.75 A resolution [Bando et al. (2004), Acta Cryst. D60, 1929-1934]. The high-resolution structure revealed conformational differences between the two enzymes in the adenosine moiety of the FAD, the lid region and the linker region. The structural properties of both proteins were inspected in terms of hydrogen bonding, ion pairs, accessible surface area and cavity volume. The differences in these structural properties between the two proteins were consistent with estimates of their thermostabilities obtained from differential scanning calorimetry data.

Organizational Affiliation

Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita, Osaka, Japan.

Macromolecule Content

Total Structure Weight: 57.88 kDa
Atom Count: 4,498
Modelled Residue Count: 486
Deposited Residue Count: 486
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-cytochrome b5 reductase	A, B	243	Physarum polycephalum	Mutation(s): 0 EC: 1.6.2.2
UniProt
Find proteins for Q1HA49 (Physarum polycephalum) Explore Q1HA49 Go to UniProtKB: Q1HA49
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q1HA49
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain G [auth A]	G [auth A], K [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain G [auth A] Focus chain K [auth B] Interactions & Density Focus chain G [auth A] Focus chain K [auth B]
IOD Query on IOD Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain C [auth A] SDF format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain C [auth A] MOL2 format, chain I [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain C [auth A] mmCIF format, chain I [auth B]	C [auth A], D [auth A], E [auth A], I [auth B]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain H [auth A]	H [auth A], L [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain L [auth B] Interactions & Density Focus chain H [auth A] Focus chain L [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B]	F [auth A], J [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.56 Å
R-Value Free: 0.226 (Depositor), 0.220 (DCC)
R-Value Work: 0.180 (Depositor), 0.190 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.084	α = 90
b = 136.369	β = 90
c = 45.718	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2007-04-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-04-17
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.3: 2023-10-25
Changes: Data collection, Database references, Derived calculations, Refinement description