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- PDB-3vym: Dimeric Hydrogenobacter thermophilus cytochrome c552 -

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Basic information

Entry
Database: PDB / ID: 3vym
TitleDimeric Hydrogenobacter thermophilus cytochrome c552
ComponentsCytochrome c-552
KeywordsELECTRON TRANSPORT
Function / homology
Function and homology information


electron transfer activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome c, class ID / Cytochrome c / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HEME C / Cytochrome c-552
Similarity search - Component
Biological speciesHydrogenobacter thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsHayashi, Y. / Nagao, S. / Osuka, H. / Komori, H. / Higuchi, Y. / Hirota, S.
CitationJournal: Biochemistry / Year: 2012
Title: Domain Swapping of the Heme and N-Terminal alpha-Helix in Hydrogenobacter thermophilus Cytochrome c(552) Dimer
Authors: Hayashi, Y. / Nagao, S. / Osuka, H. / Komori, H. / Higuchi, Y. / Hirota, S.
History
DepositionSep 28, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome c-552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,2052
Polymers8,5861
Non-polymers6191
Water57632
1
A: Cytochrome c-552
hetero molecules

A: Cytochrome c-552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4094
Polymers17,1722
Non-polymers1,2372
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_645y+1,x-1,-z1
Buried area5310 Å2
ΔGint-63 kcal/mol
Surface area9440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.148, 46.148, 78.407
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Cytochrome c-552 / Cytochrome c552


Mass: 8586.015 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hydrogenobacter thermophilus (bacteria)
Strain: TK-6 / Gene: HTH_0988, Hydth_0984 / Plasmid: pKO2 / Production host: Escherichia coli (E. coli) / Strain (production host): JCB387 / References: UniProt: P15452
#2: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.81 Å3/Da / Density % sol: 56.18 % / Mosaicity: 1.641 °
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 100mM HEPES buffer, 800mM ammonium sulfate, 45% (v/v) 2-methyl-2,4-pentanediol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 19, 2010
RadiationMonochromator: Si double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 6916 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.1 % / Rmerge(I) obs: 0.083 / Χ2: 1.531 / Net I/σ(I): 9.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.07100.8596701.0431100
2.07-2.1510.30.6886581.1591100
2.15-2.2510.40.5116771.0831100
2.25-2.3710.40.3886781.1691100
2.37-2.5210.30.2516861.222199.9
2.52-2.7110.40.196991.4641100
2.71-2.9910.30.1346641.9261100
2.99-3.4210.10.087082.119199.9
3.42-4.319.90.0557112.1811100
4.31-509.50.047651.91199.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→39.97 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.917 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.722 / SU ML: 0.129 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.176 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2635 327 4.8 %RANDOM
Rwork0.204 ---
obs0.2067 6526 99.22 %-
all-6853 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 74.82 Å2 / Biso mean: 38.3436 Å2 / Biso min: 19.66 Å2
Baniso -1Baniso -2Baniso -3
1-1.43 Å20.72 Å20 Å2
2--1.43 Å20 Å2
3----2.15 Å2
Refinement stepCycle: LAST / Resolution: 2→39.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms601 0 43 32 676
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.022668
X-RAY DIFFRACTIONr_angle_refined_deg2.1652.174914
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.05581
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.93126.36422
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.65915117
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.256151
X-RAY DIFFRACTIONr_chiral_restr0.1370.288
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021499
X-RAY DIFFRACTIONr_mcbond_it1.3031.5399
X-RAY DIFFRACTIONr_mcangle_it2.282631
X-RAY DIFFRACTIONr_scbond_it3.2353269
X-RAY DIFFRACTIONr_scangle_it5.0054.5282
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0.173 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 16 -
Rwork0.267 462 -
all-478 -
obs-478 98.15 %

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