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- PDB-3h34: PpcE, A cytochrome c7 from Geobacter sulfurreducens -

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Basic information

Entry
Database: PDB / ID: 3h34
TitlePpcE, A cytochrome c7 from Geobacter sulfurreducens
ComponentsCytochrome c7
KeywordsELECTRON TRANSPORT / cytochrome c7 / Multiheme cytochrome / Geobacter sulfurreducens
Function / homology
Function and homology information


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 superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome c
Similarity search - Component
Biological speciesGeobacter sulfurreducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsPokkuluri, P.R. / Schiffer, M.
CitationJournal: Biochim.Biophys.Acta / Year: 2010
Title: Structural characterization of a family of cytochromes c(7) involved in Fe(III) respiration by Geobacter sulfurreducens.
Authors: Pokkuluri, P.R. / Londer, Y.Y. / Yang, X. / Duke, N.E. / Erickson, J. / Orshonsky, V. / Johnson, G. / Schiffer, M.
History
DepositionApr 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Advisory / Author supporting evidence
Category: pdbx_struct_assembly_auth_evidence / pdbx_unobs_or_zero_occ_atoms
Revision 1.3Feb 21, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / 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

Downloads & links

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Assembly

Deposited unit
A: Cytochrome c7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,6834
Polymers7,8331
Non-polymers1,8493
Water1,856103
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.700, 102.000, 22.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsMonomer per asymmetric unit; Monomer in solution based on size exclusion column chromatography and dynamic light scattering

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Components

#1: Protein Cytochrome c7 / cytochrome c3


Mass: 7833.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter sulfurreducens (bacteria) / Gene: cyd-5, GSU1760 / Production host: Escherichia coli (E. coli) / Strain (production host): JCB1723 / References: UniProt: Q74CB4
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.79 Å3/Da / Density % sol: 55.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: Micro crystals obtained from SaltRx-31 (3.5 M sodium formate, 0.1 M bis-tris propane, pH 7.0) were optimized by micro seeding method, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1.73859, 1.73647, 1.78875, 1.0332
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Aug 25, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.738591
21.736471
31.788751
41.03321
ReflectionResolution: 1.6→50 Å / Num. all: 22388 / Num. obs: 22388 / % possible obs: 99 % / Redundancy: 4 % / Biso Wilson estimate: 11.5 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 28.9
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 5.5 / Num. unique all: 2226 / % possible all: 98

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Processing

Software
NameClassification
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.6→30.32 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 624877.33 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.205 2014 9.3 %RANDOM
Rwork0.19 ---
obs0.19 21637 96.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 74.2616 Å2 / ksol: 0.445928 e/Å3
Displacement parametersBiso mean: 13.3 Å2
Baniso -1Baniso -2Baniso -3
1-2 Å20 Å20 Å2
2---0.25 Å20 Å2
3----1.75 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→30.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms546 0 129 103 778
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_deg4.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.27
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.051.5
X-RAY DIFFRACTIONc_mcangle_it1.532
X-RAY DIFFRACTIONc_scbond_it1.742
X-RAY DIFFRACTIONc_scangle_it2.482.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.257 304 8.9 %
Rwork0.228 3120 -
obs-3120 91.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3hem.paramhem.top

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