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- PDB-1es1: CRYSTAL STRUCTURE OF VAL61HIS MUTANT OF TRYPSIN-SOLUBILIZED FRAGM... -

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Basic information

Entry
Database: PDB / ID: 1es1
TitleCRYSTAL STRUCTURE OF VAL61HIS MUTANT OF TRYPSIN-SOLUBILIZED FRAGMENT OF CYTOCHROME B5
ComponentsCYTOCHROME B5
KeywordsELECTRON TRANSPORT / cytochrome b5 / trypsin-cleaved fragment / mutant Val61His / crystal structure / structure comparison with the wild type fragment
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 / Resolution: 2.1 Å
AuthorsWu, J. / Gan, J.-H. / Xia, Z.-X. / Wang, Y.-H. / Wang, W.-H. / Xue, L.-L. / Xie, Y. / Huang, Z.-X.
CitationJournal: Proteins / Year: 2000
Title: Crystal structure of recombinant trypsin-solubilized fragment of cytochrome b(5) and the structural comparison with Val61His mutant.
Authors: Wu, J. / Gan, J.H. / Xia, Z.X. / Wang, Y.H. / Wang, W.H. / Xue, L.L. / Xie, Y. / Huang, Z.X.
History
DepositionApr 7, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2000Provider: repository / Type: Initial release
SupersessionNov 15, 2000ID: 1QDX
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 7, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,1312
Polymers9,5141
Non-polymers6161
Water1,35175
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.757, 40.433, 39.306
Angle α, β, γ (deg.)90.00, 111.876, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein CYTOCHROME B5


Mass: 9514.396 Da / Num. of mol.: 1 / Fragment: TRYPSIN-SOLUBILIZED FRAGMENT / Mutation: VAL61HIS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / 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.: 75 / 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: 2.74 Å3/Da / Density % sol: 55.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: phosphate buffer, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
13.2 Mphosphate1reservoirpH8.0
220 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SEALED TUBE / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→12 Å / Num. obs: 5579 / % possible obs: 91.7 % / Observed criterion σ(I): 0 / Redundancy: 1.93 % / Biso Wilson estimate: 8.1 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.3
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 1.62 % / Rmerge(I) obs: 0.232 / % possible all: 79.5

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Processing

Software
NameVersionClassification
X-PLORmodel building
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 2.1→12 Å / σ(F): 0 / Stereochemistry target values: CNS library
RfactorNum. reflectionSelection details
Rfree0.244 574 random
Rwork0.192 --
obs-5426 -
Refinement stepCycle: LAST / Resolution: 2.1→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms673 0 43 76 792
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.15
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 12 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS

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