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- PDB-3vnw: Crystal structure of cytochrome c552 from Thermus thermophilus at... -

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Basic information

Entry
Database: PDB / ID: 3vnw
TitleCrystal structure of cytochrome c552 from Thermus thermophilus at pH 5.44
ComponentsCytochrome c-552
KeywordsELECTRON TRANSPORT / Cytochrome c / Electron Transfer
Function / homology
Function and homology information


electron transfer activity / heme binding / metal ion binding
Similarity search - Function
: / 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
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome c-552
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsYamada, S. / Bouley-Ford, N.D. / Keller, G.E. / Winkler, J.R. / Gray, H.B.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Snapshots of a protein folding intermediate
Authors: Yamada, S. / Bouley-Ford, N.D. / Keller, G.E. / Ford, W.C. / Gray, H.B. / Winkler, J.R.
History
DepositionJan 18, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2013Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)14,6122
Polymers13,9951
Non-polymers6161
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.980, 86.980, 31.820
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Cytochrome c-552 / Cytochrome c552


Mass: 13995.368 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: cycA / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04164
#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.: 71 / 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: 2.45 Å3/Da / Density % sol: 49.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.44
Details: 0.2M Imidazole-Malate, 42% MPEG 5K, pH 5.44, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.97→25.68 Å / Num. all: 9951 / Num. obs: 9814 / % possible obs: 98.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 9.7
Reflection shellResolution: 1.97→2.04 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.312 / Mean I/σ(I) obs: 3.6 / Num. unique all: 956 / % possible all: 98.4

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
REFMAC5.5refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DT1

1dt1


Resolution: 1.97→20 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.903 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.202 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23243 467 4.8 %RANDOM
Rwork0.21315 ---
obs0.21406 9333 98.58 %-
all-9800 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.245 Å2
Refinement stepCycle: LAST / Resolution: 1.97→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms984 0 43 71 1098
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221051
X-RAY DIFFRACTIONr_angle_refined_deg1.2752.1111425
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5455128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.32825.38539
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.39915190
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.904153
X-RAY DIFFRACTIONr_chiral_restr0.0830.2146
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021779
X-RAY DIFFRACTIONr_mcbond_it0.6881.5635
X-RAY DIFFRACTIONr_mcangle_it1.29221003
X-RAY DIFFRACTIONr_scbond_it2.113416
X-RAY DIFFRACTIONr_scangle_it3.394.5422
LS refinement shellResolution: 1.97→2.021 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 41 -
Rwork0.272 661 -
obs-956 97.77 %

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