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- PDB-1m2i: Crystal structure of E44A/E56A mutant of cytochrome b5 -

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Basic information

Entry
Database: PDB / ID: 1m2i
TitleCrystal structure of E44A/E56A mutant of cytochrome b5
Componentscytochrome b5
KeywordsELECTRON TRANSPORT / CYTOCHROME B5 / TRYPSIN-CLEAVED FRAGMENT / MUTANT / E44A/E56A
Function / homology
Function and homology information


Vitamin C (ascorbate) metabolism / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / mitochondrial outer 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 / Roll / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome b5
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsWu, J. / Wang, Y.-H. / Gan, J.-H. / Wang, W.-H. / Sun, B.-Y. / Huang, Z.-X. / Xia, Z.-X.
CitationJournal: Chin.J.Chem. / Year: 2002
Title: Structures of Cytochrome b5 Mutated at the Charged Surface-Residues and Their Interactions with Cytochrome c
Authors: Wu, J. / Wang, Y.-H. / Gan, J.-H. / Wang, W.-H. / Sun, B.-Y. / Huang, Z.-X. / Xia, Z.-X.
History
DepositionJun 24, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _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 1.4Oct 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9762
Polymers9,3591
Non-polymers6161
Water1,63991
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.693, 40.490, 39.199
Angle α, β, γ (deg.)90.00, 111.43, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein cytochrome b5 /


Mass: 9359.308 Da / Num. of mol.: 1 / Fragment: trypsin-solubilized fragment of cytochrome b5 / Mutation: E44A, E56A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Organ: liver / Plasmid: PUC19 / Production host: Escherichia coli (E. coli) / Strain (production host): BACTERIA / References: UniProt: P00171
#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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PHOSPHATE BUFFER, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12931
22931
Diffraction source
SourceIDWavelength (Å)
SEALED TUBE11.5418
SEALED TUBE21.5418
Detector
TypeIDDetectorDate
MARRESEARCH1IMAGE PLATEDec 5, 1997
MARRESEARCH2IMAGE PLATEApr 3, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→19.9 Å / Num. obs: 8616 / % possible obs: 88.9 % / Biso Wilson estimate: 18.3 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 18.2
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.228 / % possible all: 56.3

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1M20

1m20


Resolution: 1.8→19.9 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.232 915 10.6 %RANDOM
Rwork0.193 ---
obs0.193 8616 88.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 104.932 Å2 / ksol: 0.628754 e/Å3
Displacement parametersBiso mean: 25.1 Å2
Baniso -1Baniso -2Baniso -3
1-6.63 Å20 Å2-1 Å2
2---2.81 Å20 Å2
3----3.82 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.22 Å
Luzzati sigma a0.19 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.8→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms662 0 43 91 796
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.1
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.41.5
X-RAY DIFFRACTIONc_mcangle_it2.072
X-RAY DIFFRACTIONc_scbond_it2.582
X-RAY DIFFRACTIONc_scangle_it3.992.5
LS refinement shellResolution: 1.8→1.86 Å / Rfactor Rfree error: 0.041 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.317 58 10.7 %
Rwork0.288 485 -
obs--56.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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