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- PDB-1u9m: Crystal structure of F58W mutant of cytochrome b5 -

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Basic information

Entry
Database: PDB / ID: 1u9m
TitleCrystal structure of F58W mutant of cytochrome b5
ComponentsCytochrome b5
KeywordsELECTRON TRANSPORT / hemoprotein / F58Y and F58W mutants / conformational changes / aromatic-aromatic interactions / structure-function relationship
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsShan, L. / Lu, J.-X. / Gan, J.-H. / Wang, Y.-H. / Huang, Z.-X. / Xia, Z.-X.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Structure of the F58W mutant of cytochrome b5: the mutation leads to multiple conformations and weakens stacking interactions.
Authors: Shan, L. / Lu, J.X. / Gan, J.H. / Wang, Y.H. / Huang, Z.X. / Xia, Z.X.
History
DepositionAug 10, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome b5
B: Cytochrome b5
C: Cytochrome b5
D: Cytochrome b5
E: Cytochrome b5
F: Cytochrome b5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,78512
Polymers57,0866
Non-polymers3,6996
Water2,702150
1
A: Cytochrome b5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,1312
Polymers9,5141
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome b5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,1312
Polymers9,5141
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cytochrome b5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,1312
Polymers9,5141
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cytochrome b5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,1312
Polymers9,5141
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Cytochrome b5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,1312
Polymers9,5141
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Cytochrome b5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,1312
Polymers9,5141
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.044, 87.484, 138.383
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: 9514.416 Da / Num. of mol.: 6 / Fragment: trypsin-solubilized fragment / Mutation: F58W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / 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.: 6 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.34 Å3/Da / Density % sol: 52.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: phosphate buffer, dioxane, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.97891 Å
DetectorDetector: CCD / Date: Dec 2, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97891 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 45329 / Num. obs: 40502 / % possible obs: 87.3 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.095
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.571 / Num. unique all: 4494 / % possible all: 99.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1EHB

1ehb


Resolution: 2→35.55 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 230984.86 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.266 3877 10.2 %RANDOM
Rwork0.224 ---
obs0.224 38189 96.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.8144 Å2 / ksol: 0.360604 e/Å3
Displacement parametersBiso mean: 32.5 Å2
Baniso -1Baniso -2Baniso -3
1-4.15 Å20 Å20 Å2
2---10.98 Å20 Å2
3---6.83 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2→35.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4080 0 258 150 4488
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_mcbond_it1.541.5
X-RAY DIFFRACTIONc_mcangle_it2.392
X-RAY DIFFRACTIONc_scbond_it2.232
X-RAY DIFFRACTIONc_scangle_it3.422.5
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.313 391 10.7 %
Rwork0.269 3268 -
obs--94.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3PARAM19X.HEMHEME.TOP
X-RAY DIFFRACTION4&_1_PARAMETER_INFILE_4&_1_TOPOLOGY_INFILE_4
X-RAY DIFFRACTION5&_1_PARAMETER_INFILE_5&_1_TOPOLOGY_INFILE_5

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