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- PDB-7bwh: Soluble cytochrome b5 from Ramazzottius varieornatus -

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Basic information

Entry
Database: PDB / ID: 7bwh
TitleSoluble cytochrome b5 from Ramazzottius varieornatus
ComponentsCytochrome b5 heme-binding domain-containing protein
KeywordsELECTRON TRANSPORT / heme protein / cytochrome b5
Function / homology
Function and homology information


Flavocytochrome B2; Chain A, domain 1 / Cytochrome b5-like heme/steroid binding domain / Cytochrome b5 family, heme-binding domain profile. / Cytochrome 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 / Roll / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome b5 heme-binding domain-containing protein
Similarity search - Component
Biological speciesRamazzottius varieornatus (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å
AuthorsKim, J. / Inoue, T. / Fukuda, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJAX191C Japan
CitationJournal: Protein Sci. / Year: 2020
Title: Structure of cytochrome b5unique to tardigrades.
Authors: Fukuda, Y. / Kim, J. / Inoue, T.
History
DepositionApr 14, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 5, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome b5 heme-binding domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4353
Polymers12,7831
Non-polymers6522
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-21 kcal/mol
Surface area5650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.004, 37.495, 77.546
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-378-

HOH

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Components

#1: Protein Cytochrome b5 heme-binding domain-containing protein


Mass: 12783.229 Da / Num. of mol.: 1 / Fragment: UNP residues 10-102
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ramazzottius varieornatus (invertebrata)
Gene: RvY_13572-1, RvY_13572.1, RvY_13572 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A1D1VNB4
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 1.93 Å3/Da / Density % sol: 36.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 26 mg/mL protein, 22% (w/v) PEG 4000, and 50 mM HEPES buffer pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.4→38.8 Å / Num. obs: 20165 / % possible obs: 99.7 % / Redundancy: 6.3 % / Biso Wilson estimate: 15.47 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.016 / Rrim(I) all: 0.039 / Net I/σ(I): 24
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 965 / CC1/2: 0.871 / Rpim(I) all: 0.196 / Rrim(I) all: 0.493 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMACCCP4Interface 7.0.078refinement
XDSdata reduction
Aimlessdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.4→38.8 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.171 -5 %
Rwork0.147 --
obs-19138 99.6 %
Displacement parametersBiso mean: 28.45 Å2
Refinement stepCycle: LAST / Resolution: 1.4→38.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms693 0 44 95 832
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0168968
X-RAY DIFFRACTIONf_angle_d1.44891365
X-RAY DIFFRACTIONf_chiral_restr0.0918119
X-RAY DIFFRACTIONf_plane_restr0.0065165
X-RAY DIFFRACTIONf_dihedral_angle_d22.1834332

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