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- PDB-19hc: NINE-HAEM CYTOCHROME C FROM DESULFOVIBRIO DESULFURICANS ATCC 27774 -

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Basic information

Entry
Database: PDB / ID: 19hc
TitleNINE-HAEM CYTOCHROME C FROM DESULFOVIBRIO DESULFURICANS ATCC 27774
ComponentsPROTEIN (NINE-HAEM CYTOCHROME C)
KeywordsELECTRON TRANSPORT / ELECTRON TRANSFER / CYTOCHROME
Function / homology
Function and homology information


periplasmic space / electron transfer activity / heme binding / metal ion binding
Similarity search - Function
Class III cytochrome C / Class III cytochrome C family / Cytochrome c, class III / Cytochrome C3 / Cytochrome C3 / Multiheme cytochrome c family profile. / Multiheme cytochrome superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / PROTOPORPHYRIN IX CONTAINING FE / Nine-heme cytochrome c
Similarity search - Component
Biological speciesDesulfovibrio desulfuricans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsMatias, P.M. / Coelho, R. / Pereira, I.A.C. / Coelho, A.V. / Thompson, A.W. / Sieker, L. / Gall, J.L. / Carrondo, M.A.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: The primary and three-dimensional structures of a nine-haem cytochrome c from Desulfovibrio desulfuricans ATCC 27774 reveal a new member of the Hmc family.
Authors: Matias, P.M. / Coelho, R. / Pereira, I.A. / Coelho, A.V. / Thompson, A.W. / Sieker, L.C. / Gall, J.L. / Carrondo, M.A.
History
DepositionDec 1, 1998Deposition site: PDBE / Processing site: RCSB
Revision 1.0Dec 1, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 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: PROTEIN (NINE-HAEM CYTOCHROME C)
B: PROTEIN (NINE-HAEM CYTOCHROME C)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,97325
Polymers62,5812
Non-polymers11,39223
Water15,943885
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25780 Å2
ΔGint-445 kcal/mol
Surface area27400 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)60.380, 106.070, 80.620
Angle α, β, γ (deg.)90.00, 103.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PROTEIN (NINE-HAEM CYTOCHROME C)


Mass: 31290.666 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Desulfovibrio desulfuricans (bacteria) / Cellular location: PERIPLASMIC (PRESUMED) / References: UniProt: Q9RN68
#2: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 885 / 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: 3.42 Å3/Da / Density % sol: 64 %
Crystal growpH: 5.5
Details: PEG 6000 2-10% (W/V) SODIUM ACETATE BUFFER PH 5.5 0.25-0.75M
Crystal grow
*PLUS
Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: Coelho, A.V., (1996) Acta Crystallogr. D52, 1202.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12-10 %(v/v)PEG60001reservoir
20.25-0.75 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.7377, 1.7398, 1.7408, 0.8856
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1998 / Details: MIRRORS
RadiationMonochromator: SI (111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.73771
21.73981
31.74081
40.88561
ReflectionResolution: 1.8→24.2 Å / Num. obs: 91192 / % possible obs: 98.8 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 16.8
Reflection shellResolution: 1.8→1.87 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.116 / Mean I/σ(I) obs: 6.2 / % possible all: 93.1
Reflection
*PLUS
Num. measured all: 425233
Reflection shell
*PLUS
% possible obs: 93.1 %

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Processing

Software
NameClassification
CCP4model building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→24 Å / Num. parameters: 24762 / Num. restraintsaints: 24527 / Cross valid method: NONE IN LAST CYCLES / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28 (1995)53-56
RfactorNum. reflection% reflection
obs0.1694 -98.8 %
all-91192 -
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 14 / Occupancy sum non hydrogen: 5876.5
Refinement stepCycle: LAST / Resolution: 1.8→24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4419 0 794 885 6098
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.024
X-RAY DIFFRACTIONs_similar_dist0.006
X-RAY DIFFRACTIONs_from_restr_planes0.029
X-RAY DIFFRACTIONs_zero_chiral_vol0.113
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.116
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.007
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.044
X-RAY DIFFRACTIONs_approx_iso_adps

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