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- PDB-1x3x: Crystal Structure of Cytochrome b5 from Ascaris suum -

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Basic information

Entry
Database: PDB / ID: 1x3x
TitleCrystal Structure of Cytochrome b5 from Ascaris suum
ComponentsCytochrome b5
KeywordsELECTRON TRANSPORT / cytochrome b5 / hemoprotein / porcine parasitic namatode
Function / homology
Function and homology information


Flavocytochrome B2; Chain A, domain 1 / Cytochrome b5-like heme/steroid binding domain / 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 speciesAscaris suum (pig roundworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsYokota, T. / Nakajima, Y. / Yamakura, F. / Sugio, S. / Hashimoto, M. / Takamiya, S. / Aoki, T.
CitationJournal: Biochem.J. / Year: 2006
Title: Unique structure of Ascaris suum b5-type cytochrome: an additional alpha-helix and positively charged residues on the surface domain interact with redox partners
Authors: Yokota, T. / Nakajima, Y. / Yamakura, F. / Sugio, S. / Hashimoto, M. / Takamiya, S.
History
DepositionMay 11, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 6, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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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)19,6485
Polymers18,3192
Non-polymers1,3293
Water4,089227
1
A: Cytochrome b5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,7762
Polymers9,1601
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome b5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,8723
Polymers9,1601
Non-polymers7132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.225, 41.774, 49.763
Angle α, β, γ (deg.)90.00, 111.13, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is monomer.

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Components

#1: Protein Cytochrome b5 /


Mass: 9159.631 Da / Num. of mol.: 2 / Fragment: Residues 1-82
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ascaris suum (pig roundworm) / Plasmid: pET-28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q17091
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 2.71 Å3/Da / Density % sol: 54.6 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: ammonium sulfate, sodium phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU RU30011.5418
SYNCHROTRONPhoton Factory BL-18B21.7395, 1.7390, 1.7000
Detector
TypeIDDetectorDate
RIGAKU RAXIS IIC1IMAGE PLATE
ADSC QUANTUM 42CCDJun 6, 2002
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1graphiteSINGLE WAVELENGTHMx-ray1
2Si(111)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
21.73951
31.7391
41.71
ReflectionResolution: 1.8→50 Å / Num. all: 17915 / Num. obs: 17915 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.051 / Net I/σ(I): 42.1
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.179 / Mean I/σ(I) obs: 9.5 / Num. unique all: 1691 / % possible all: 93.5

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
CNS1.1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.8→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.236 921 -random
Rwork0.192 ---
all-17891 --
obs-17891 96.6 %-
Displacement parametersBiso mean: 19.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.07 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1282 0 91 227 1600
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d1.263
X-RAY DIFFRACTIONc_improper_angle_d20.86
X-RAY DIFFRACTIONc_dihedral_angle_d0.6558
LS refinement shellResolution: 1.8→1.86 Å
RfactorNum. reflection% reflection
Rfree0.278 92 -
Rwork0.222 --
obs-1677 92.7 %

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