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- PDB-1lr6: Crystal structure of V45Y mutant of cytochrome b5 -

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Basic information

Entry
Database: PDB / ID: 1lr6
TitleCrystal structure of V45Y mutant of cytochrome b5
Componentscytochrome b5
KeywordsELECTRON TRANSPORT / CYTOCHROME B5 / TRYPSIN-SOLUBILIZED FRAGMENT / MUTANT V45Y
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 speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsGan, J.-H. / Wu, J. / Wang, Z.-Q. / Wang, Y.-H. / Huang, Z.-X. / Xia, Z.-X.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Structures of V45E and V45Y mutants and structure comparison of a variety of cytochrome b5 mutants.
Authors: Gan, J.H. / Wu, J. / Wang, Z.Q. / Wang, Y.H. / Huang, Z.X. / Xia, Z.X.
History
DepositionMay 15, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 4, 2002Provider: 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

Downloads & links

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Assembly

Deposited unit
A: cytochrome b5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,1562
Polymers9,5391
Non-polymers6161
Water1,62190
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.404, 40.441, 39.196
Angle α, β, γ (deg.)90.00, 111.70, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein cytochrome b5


Mass: 9539.423 Da / Num. of mol.: 1 / Fragment: trypsin-solubilized fragment of cytochrome b5 / Mutation: V45Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Organ: liver / Plasmid: pU19 / Production host: Escherichia coli (E. coli) / References: UniProt: P00171
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.68 Å3/Da / Density % sol: 54.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PHOSPHATE BUFFER, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal grow
*PLUS
Temperature: 293 K
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
23.1 Mphosphate1reservoirpH7.5

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SEALED TUBE / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 10, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→22.82 Å / Num. obs: 7563 / % possible obs: 93.5 % / Redundancy: 3.1 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.062
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.194 / Mean I/σ(I) obs: 6.1 / % possible all: 76.3
Reflection
*PLUS
Highest resolution: 1.9 Å / Rmerge(I) obs: 0.062
Reflection shell
*PLUS
% possible obs: 76.3 % / Rmerge(I) obs: 0.194

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Processing

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

1ehb


Resolution: 1.9→22.82 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.236 782 10.7 %RANDOM
Rwork0.191 ---
all0.196 ---
obs0.191 7336 90.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 66.6757 Å2 / ksol: 0.402579 e/Å3
Displacement parametersBiso mean: 29.1 Å2
Baniso -1Baniso -2Baniso -3
1-11.38 Å20 Å22.22 Å2
2---5.8 Å20 Å2
3----5.58 Å2
Refine analyzeLuzzati coordinate error free: 0.27 Å / Luzzati sigma a free: 0.19 Å
Refinement stepCycle: LAST / Resolution: 1.9→22.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms675 0 43 90 808
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
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_d22.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.99
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.9→1.97 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.274 62 10.8 %
Rwork0.289 513 -
obs--71.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 1.9 Å / Rfactor all: 0.196 / Rfactor obs: 0.191 / Rfactor Rfree: 0.235 / Rfactor Rwork: 0.192
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.165
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.99
LS refinement shell
*PLUS
Rfactor Rfree: 0.274 / Rfactor Rwork: 0.289

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