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- PDB-1h1o: Acidithiobacillus ferrooxidans cytochrome c4 structure supports a... -

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Basic information

Entry
Database: PDB / ID: 1h1o
TitleAcidithiobacillus ferrooxidans cytochrome c4 structure supports a complex-induced tuning of electron transfer
ComponentsCYTOCHROME C-552
KeywordsELECTRON TRANSPORT / C4 / CYTOCHROME / ELECTRON TRANSFER / HEME
Function / homology
Function and homology information


electron transfer activity / periplasmic space / iron ion binding / heme binding
Similarity search - Function
Cytochrome c4-like / 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 speciesTHIOBACILLUS FERROOXIDANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.13 Å
AuthorsAbergel, C. / Nitschke, W. / Malarte, G. / Bruschi, M. / Claverie, J.-M. / Guidici-Orticoni, M.-T.
CitationJournal: Structure / Year: 2003
Title: The Structure of Acidithiobacillus Ferrooxidans C(4)-Cytochrome. A Model for Complex-Induced Electron Transfer Tuning
Authors: Abergel, C. / Nitschke, W. / Malarte, G. / Bruschi, M. / Claverie, J.-M. / Guidici-Orticoni, M.-T.
History
DepositionJul 19, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2003Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2011Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CYTOCHROME C-552
B: CYTOCHROME C-552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,01615
Polymers39,8732
Non-polymers3,14313
Water3,351186
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A: CYTOCHROME C-552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4627
Polymers19,9371
Non-polymers1,5256
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CYTOCHROME C-552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5548
Polymers19,9371
Non-polymers1,6177
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)100.049, 100.049, 149.668
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-2022-

HOH

21A-2053-

HOH

31A-2112-

HOH

41A-2115-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein CYTOCHROME C-552 / C552 / CYTOCHROME C4


Mass: 19936.615 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THIOBACILLUS FERROOXIDANS (bacteria) / References: UniProt: P74917

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Non-polymers , 5 types, 199 molecules

#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsBELONGS TO THE CLASS C4 FAMILY OF CYTOCHROMES WITH TWO BOUND HEME MOLECULES PER MOLECULE OF PROTEIN.
Sequence detailsMATURE SEQUENCE WITHOUT SIGNAL PEPTIDE NEW NAME PROPOSED: CYC4_THIFE

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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: 2.7 Å3/Da / Density % sol: 56 %
Crystal growpH: 6.5
Details: MES 0.1M PH 6.5, PEG MME 30%, 10MM ZINC SULFATE, 5% GLYCEROL
Crystal grow
*PLUS
pH: 2.9 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
220 mMglycine-HCl1droppH2.9
31 mMascorbate1drop
40.1 MMES1reservoirpH6.5
525-30 %PEG MME1reservoir
610 mMzinc sulfate1reservoir
71 mMascorbate1reservoir
85 %glycerol1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONESRF BM30A11.74
SYNCHROTRONESRF ID14-120.98
Detector
IDDate
1May 15, 2000
2
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2x-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.741
20.981
ReflectionResolution: 2.13→25 Å / Num. obs: 25043 / % possible obs: 99.7 % / Redundancy: 4.9 % / Biso Wilson estimate: 36.4 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 8.2
Reflection shellResolution: 2.13→2.2 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.315 / Mean I/σ(I) obs: 2.3 / % possible all: 99.7
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 35 Å / Num. obs: 23012 / Redundancy: 4.9 % / Num. measured all: 112983 / Rmerge(I) obs: 0.041
Reflection shell
*PLUS
% possible obs: 99.7 % / Redundancy: 5 % / Rmerge(I) obs: 0.245 / Mean I/σ(I) obs: 3.1

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.13→25 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2693270.24 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: RESIDUES 1 - 11 IN THE FIRST MOLECULE AND 201 - 212 IN THE SECOND MOLECULE ARE DESORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.284 2504 9.9 %RANDOM
Rwork0.239 ---
obs0.239 25292 99.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.9213 Å2 / ksol: 0.364664 e/Å3
Displacement parametersBiso mean: 45.8 Å2
Baniso -1Baniso -2Baniso -3
1-7.03 Å26.17 Å20 Å2
2--7.03 Å20 Å2
3----14.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.13→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2618 0 194 186 2998
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.281.5
X-RAY DIFFRACTIONc_mcangle_it2.142
X-RAY DIFFRACTIONc_scbond_it1.92
X-RAY DIFFRACTIONc_scangle_it2.752.5
LS refinement shellResolution: 2.13→2.26 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.326 402 9.7 %
Rwork0.294 3728 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3HEM.PARAMHEM.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 35 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.84

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