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- PDB-3x32: Crystal structure of the oxidized form of the solubilized domain ... -

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Basic information

Entry
Database: PDB / ID: 3x32
TitleCrystal structure of the oxidized form of the solubilized domain of porcine cytochrome b5 in form 1 crystal
ComponentsCytochrome b5
KeywordsELECTRON TRANSPORT / HEME
Function / homology
Function and homology information


Vitamin C (ascorbate) metabolism / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane / metal ion binding
Similarity search - Function
: / Flavocytochrome B2; Chain A, domain 1 / Cytochrome b5-like heme/steroid binding domain / Cytochrome b5, heme-binding site / Cytochrome b5 family, heme-binding domain signature. / 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 ...: / Flavocytochrome B2; Chain A, domain 1 / Cytochrome b5-like heme/steroid binding domain / Cytochrome b5, heme-binding site / Cytochrome b5 family, heme-binding domain signature. / 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
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.83 Å
AuthorsHirano, Y. / Kimura, S. / Tamada, T.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: High-resolution crystal structures of the solubilized domain of porcine cytochrome b5.
Authors: Hirano, Y. / Kimura, S. / Tamada, T.
History
DepositionJan 14, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Dec 25, 2019Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_CSD ..._citation.country / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome b5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7065
Polymers10,7711
Non-polymers9354
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.339, 39.279, 60.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cytochrome b5


Mass: 10770.889 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN, UNP residues 1-94
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: CYB5A, CYB5 / Plasmid: pCPb5 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P00172
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O

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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: 1.8 Å3/Da / Density % sol: 31.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 24% PEG 1500, 4% 2-propanol, 0.1M calcium chloride, 0.1M HEPES-NaOH, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.91 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 9, 2014
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 0.83→50 Å / Num. all: 73045 / Num. obs: 72789 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.5 % / Biso Wilson estimate: 6.2 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 59.8
Reflection shellResolution: 0.83→0.84 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 7.6 / % possible all: 82.3

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Processing

Software
NameClassification
SERGUIdata collection
PHASERphasing
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CYO

1cyo


Resolution: 0.83→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.127 3652 RANDOM
Rwork0.106 --
all0.109 72972 -
obs0.107 72735 -
Refinement stepCycle: LAST / Resolution: 0.83→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms705 0 60 214 979
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d0.04
X-RAY DIFFRACTIONs_bond_d0.037
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.099
X-RAY DIFFRACTIONs_from_restr_planes0.37

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