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- PDB-6vz6: Methanococcoides burtonii cytochrome b5 domain protein (WP 011499... -

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Basic information

Entry
Database: PDB / ID: 6vz6
TitleMethanococcoides burtonii cytochrome b5 domain protein (WP 011499504.1)
ComponentsCytochrome b5-domain protein
KeywordsMETAL BINDING PROTEIN / heme binding / cytochrome b5 domain
Function / homologyCytochrome b5-like heme/steroid binding domain / Cytochrome b5-like heme/steroid binding domain superfamily / Cytochrome b5-like Heme/Steroid binding domain / Cytochrome b5-like Heme/Steroid binding domain / metal ion binding / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome b5-domain protein
Function and homology information
Biological speciesMethanococcoides burtonii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsTeakel, S.L. / Forwood, J.K. / Aragao, D. / Cahill, M.A. / Marama, M.
CitationJournal: To Be Published
Title: Methanococcoides burtonii cytochrome b5 domain protein (WP 011499504.1)
Authors: Teakel, S.L. / Forwood, J.K. / Aragao, D. / Cahill, M.A. / Marama, M.
History
DepositionFeb 27, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2023Group: Database references / Structure summary / Category: audit_author / citation_author / database_2
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome b5-domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3832
Polymers8,7661
Non-polymers6161
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.495, 67.495, 48.132
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Space group name HallP4w2c
Components on special symmetry positions
IDModelComponents
11A-237-

HOH

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Components

#1: Protein Cytochrome b5-domain protein


Mass: 8766.481 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanococcoides burtonii (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: Q12W16
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.13 Å3/Da / Density % sol: 60.66 %
Crystal growTemperature: 296.15 K / Method: vapor diffusion, hanging drop / Details: 0.1M succinic acid, 12% PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.1→67.5 Å / Num. obs: 6719 / % possible obs: 98 % / Redundancy: 7.1 % / Biso Wilson estimate: 21.47 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.033 / Rrim(I) all: 0.096 / Net I/σ(I): 14.3
Reflection shellResolution: 2.101→23.863 Å / Num. unique obs: 6717 / CC1/2: 0.997

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
Aimlessdata scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NZX

6nzx


Resolution: 2.1→23.86 Å / SU ML: 0.1736 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.9772 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1953 317 4.72 %
Rwork0.1622 6400 -
obs0.1638 6717 97.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.84 Å2
Refinement stepCycle: LAST / Resolution: 2.1→23.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms609 0 43 66 718
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0139682
X-RAY DIFFRACTIONf_angle_d1.3027937
X-RAY DIFFRACTIONf_chiral_restr0.065986
X-RAY DIFFRACTIONf_plane_restr0.0077122
X-RAY DIFFRACTIONf_dihedral_angle_d6.6771518
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.650.20541520.16423070X-RAY DIFFRACTION96.41
2.65-23.860.19091650.16133330X-RAY DIFFRACTION98.7

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