1M70 | pdb_00001m70

Crystal structure of oxidized recombinant cytochrome c4 from Pseudomonas stutzeri

PDB DOI: https://doi.org/10.2210/pdb1M70/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Stutzerimonas stutzeri
Expression System: Pseudomonas putida
Mutation(s): No
Membrane Protein: Yes OPM

Deposited: 2002-07-18 Released: 2003-09-16
Deposition Author(s): Noergaard, A., Harris, P., Larsen, S., Christensen, H.E.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free:
0.202 (Depositor), 0.171 (DCC)
R-Value Work:
0.155 (Depositor), 0.160 (DCC)
R-Value Observed:
0.157 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Structural comparison of recombinant Pseudomonas stutzeri cytochrome c4 in two oxidation states

Noergaard, A., Harris, P., Larsen, S., Christensen, H.E.M.

To be published.

Macromolecule Content

Total Structure Weight: 83.84 kDa
Atom Count: 6,717
Modeled Residue Count: 760
Deposited Residue Count: 760
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c4	A, B, C, D	190	Stutzerimonas stutzeri	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q52369 (Stutzerimonas stutzeri) Explore Q52369 Go to UniProtKB: Q52369
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q52369
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEC Query on HEC Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth C] SDF format, chain K [auth C] SDF format, chain L [auth D] SDF format, chain M [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth C] MOL2 format, chain K [auth C] MOL2 format, chain L [auth D] MOL2 format, chain M [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth C] mmCIF format, chain K [auth C] mmCIF format, chain L [auth D] mmCIF format, chain M [auth D]	E [auth A] F [auth A] H [auth B] I [auth B] J [auth C] E [auth A], F [auth A], H [auth B], I [auth B], J [auth C], K [auth C], L [auth D], M [auth D]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free: 0.202 (Depositor), 0.171 (DCC)
R-Value Work: 0.155 (Depositor), 0.160 (DCC)
R-Value Observed: 0.157 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.96	α = 90
b = 57.64	β = 104.23
c = 84.41	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
SHELXL-97	refinement

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2003-09-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2003-09-16
Type: Initial release
Version 1.1: 2008-04-28
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.3: 2018-05-23
Changes: Data collection
Version 1.4: 2023-10-25
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.5: 2024-10-23
Changes: Structure summary

1M70 | pdb_00001m70

Crystal structure of oxidized recombinant cytochrome c4 from Pseudomonas stutzeri

Literature

Structural comparison of recombinant Pseudomonas stutzeri cytochrome c4 in two oxidation states

Biological Assembly 1

Biological Assembly 2

Biological Assembly 3

Biological Assembly 4

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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