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- PDB-3ner: Structure of Human Type B Cytochrome b5 -

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Basic information

Entry
Database: PDB / ID: 3ner
TitleStructure of Human Type B Cytochrome b5
ComponentsCytochrome b5 type B
KeywordsELECTRON TRANSPORT / CYTOCHROME B5 / HEME
Function / homology
Function and homology information


nitric-oxide synthase complex / Sphingolipid de novo biosynthesis / Phase I - Functionalization of compounds / eNOS activation / nitric oxide biosynthetic process / xenobiotic metabolic process / enzyme activator activity / response to oxidative stress / mitochondrial outer membrane / intracellular membrane-bounded organelle ...nitric-oxide synthase complex / Sphingolipid de novo biosynthesis / Phase I - Functionalization of compounds / eNOS activation / nitric oxide biosynthetic process / xenobiotic metabolic process / enzyme activator activity / response to oxidative stress / mitochondrial outer membrane / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane / metal ion binding / membrane
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 type B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsTerzyan, S. / Zhang, C. / Rivera, M. / Benson, D.B.
CitationJournal: Biochemistry / Year: 2011
Title: Accommodating a Non-Conservative Internal Mutation by Water-Mediated Hydrogen-Bonding Between beta-Sheet Strands: A Comparison of Human and Rat Type B (Mitochondrial) Cytochrome b5
Authors: Parthasarathy, S. / Altuve, A. / Terzyan, S. / Zhang, X. / Kuczera, K. / Rivera, M. / Benson, D.R.
History
DepositionJun 9, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Sep 6, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

Downloads & links

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Assembly

Deposited unit
A: Cytochrome b5 type B
B: Cytochrome b5 type B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4536
Polymers21,0992
Non-polymers1,3534
Water5,350297
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-64 kcal/mol
Surface area11980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.316, 40.034, 58.744
Angle α, β, γ (deg.)90.00, 98.61, 90.00
Int Tables number4
Space group name H-MP1211
Details1

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Components

#1: Protein Cytochrome b5 type B / Cytochrome b5 outer mitochondrial membrane isoform


Mass: 10549.634 Da / Num. of mol.: 2
Fragment: N-TERMINAL HEME-BINDING DOMAIN (UNP RESIDUES 12-103)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYB5B, CYB5M, OMB5 / Plasmid: pet11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O43169
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / 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: 2.06 Å3/Da / Density % sol: 40.18 %
Crystal growTemperature: 278 K / pH: 6.8
Details: 30% PEG8K, 0.1M Hepes (pH 6.8) and 0.2M magnesium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.976
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 8, 2004 / Details: MONOCHROMATOR
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.45→29.24 Å / Num. obs: 29891 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 17.84 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 18.45
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.453 / Mean I/σ(I) obs: 2.13

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LJ0

1lj0


Resolution: 1.45→29.24 Å / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.215 1131 -RANDOM
Rwork0.177 ---
obs0.177 28569 93.3 %-
all-29891 --
Solvent computationBsol: 59.33 Å2 / ksol: 0.48 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.227 Å20 Å2-2.896 Å2
2--1.325 Å20 Å2
3---0.902 Å2
Refine analyzeLuzzati coordinate error obs: 0.11 Å
Refinement stepCycle: LAST / Resolution: 1.45→29.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1459 0 92 297 1848
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.019
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.481
X-RAY DIFFRACTIONc_mcangle_it2.166
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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