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- PDB-1awp: RAT OUTER MITOCHONDRIAL MEMBRANE CYTOCHROME B5 -

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Basic information

Entry
Database: PDB / ID: 1awp
TitleRAT OUTER MITOCHONDRIAL MEMBRANE CYTOCHROME B5
ComponentsCYTOCHROME B5
KeywordsELECTRON TRANSPORT / CYTOCHROME / HEME
Function / homology
Function and homology information


Sphingolipid de novo biosynthesis / Phase I - Functionalization of compounds / nitric-oxide synthase complex / nitrite reductase (NO-forming) activity / ubiquinol-cytochrome-c reductase activity / enzyme activator activity / nitric oxide biosynthetic process / mitochondrial outer membrane / intracellular membrane-bounded organelle / heme binding / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome b5 type B
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWang, X. / Zhang, X.
CitationJournal: Biochemistry / Year: 1998
Title: The reduction potential of cytochrome b5 is modulated by its exposed heme edge.
Authors: Rivera, M. / Seetharaman, R. / Girdhar, D. / Wirtz, M. / Zhang, X. / Wang, X. / White, S.
History
DepositionOct 3, 1997Processing site: BNL
Revision 1.0Oct 28, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 2, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYTOCHROME B5
B: CYTOCHROME B5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0724
Polymers20,8392
Non-polymers1,2332
Water1,856103
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.640, 71.190, 73.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.54813, 0.5997, 0.58302), (-0.83443, -0.43982, -0.33209), (0.05727, -0.66852, 0.74149)
Vector: -9.96452, 88.53668, 11.72105)

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Components

#1: Protein CYTOCHROME B5


Mass: 10419.405 Da / Num. of mol.: 2 / Fragment: WATER SOLUBLE DOMAIN / Mutation: V45L, V61L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell: HEPATOCYTE / Cell line: BL21 / Cellular location: OUTER MITOCHONDRIAL MEMBRANE / Gene: POTENTIAL / Organ: LIVER / Organelle: MITOCHONDRION / Plasmid: PET 11A / Species (production host): Escherichia coli / Cellular location (production host): PERIPLASMIC SPACE / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P04166
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.7 Å3/Da / Density % sol: 54 %
Crystal
*PLUS
Crystal grow
*PLUS
pH: 7.8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mMTRIS1drop
20.1 %sodium azide1drop
320 mg/mlprotein1drop
430 %PEG8000 MW1reservoir
50.20 Mmagnesium acetate1reservoir
60.10 MPIPES1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Jun 1, 1997
RadiationMonochromator: CRYSTAL / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→10 Å / Num. obs: 16374 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 19.6 Å2 / Rsym value: 0.075 / Net I/σ(I): 32.42
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.18 % / Mean I/σ(I) obs: 3.41 / Rsym value: 0.274 / % possible all: 92.5
Reflection
*PLUS
Rmerge(I) obs: 0.075
Reflection shell
*PLUS
% possible obs: 84.7 % / Rmerge(I) obs: 0.274

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
SAINTdata reduction
SAINTdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1B5M

1b5m


Resolution: 2→8 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
Details: NCS RESTRAINTS WERE USED IN INITIAL STEP OF REFINEMENT. BULK SOLVENT MODELING METHOD WAS USED.
RfactorNum. reflection% reflectionSelection details
Rfree0.225 -9.75 %RANDOM
Rwork0.1802 ---
obs0.1802 16087 97.4 %-
Displacement parametersBiso mean: 37.3 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å / Luzzati d res low obs: 8 Å
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1386 0 86 103 1575
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.156
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.565
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2→2.09 Å
RfactorNum. reflection% reflection
Rfree0.3356 -9.91 %
Rwork0.3098 1676 -
obs--92.96 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2HEM.PARHEM.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.2259
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.565

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