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- PDB-3ov0: Structure of dodecaheme cytochrome c GSU1996 -

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Basic information

Entry
Database: PDB / ID: 3ov0
TitleStructure of dodecaheme cytochrome c GSU1996
ComponentsCytochrome c family protein
KeywordsELECTRON TRANSPORT / multiheme cytochrome c / electron transfer / Fe reduction / Geobacter sulfurreducens / cytochrome c7 (c3) fold domains / protein composed of cytochrome c7 (c3) fold domains
Function / homology
Function and homology information


C(7)-type cytochrome triheme domain / Cytochrome c7-like / Cytochrome c7 and related cytochrome c / Cytochrome C3 / Cytochrome C3 / Multiheme cytochrome superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
HEME C / Cytochrome c
Similarity search - Component
Biological speciesGeobacter sulfurreducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.2 Å
AuthorsPokkuluri, P.R. / Schiffer, M.
Citation
Journal: J.Struct.Biol. / Year: 2011
Title: Structure of a novel dodecaheme cytochrome c from Geobacter sulfurreducens reveals an extended 12nm protein with interacting hemes.
Authors: Pokkuluri, P.R. / Londer, Y.Y. / Duke, N.E. / Pessanha, M. / Yang, X. / Orshonsky, V. / Orshonsky, L. / Erickson, J. / Zagyanskiy, Y. / Salgueiro, C.A. / Schiffer, M.
#1: Journal: Protein Sci. / Year: 2004
Title: Structure of a novel c7-type three-heme cytochrome domain from a multi-domain cytochrome polymer
Authors: R Pokkuluri, P. / Londer, Y.Y. / Duke, N.E. / Erickson, J. / Pessanha, M. / Salgueiro, C.A. / Schiffer, M.
History
DepositionSep 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Mar 3, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_validate_close_contact.auth_comp_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome c family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,37713
Polymers34,9551
Non-polymers7,42212
Water1629
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Cytochrome c family protein
hetero molecules

A: Cytochrome c family protein
hetero molecules

A: Cytochrome c family protein
hetero molecules

A: Cytochrome c family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,50752
Polymers139,8194
Non-polymers29,68848
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area61260 Å2
ΔGint-1169 kcal/mol
Surface area66870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.900, 150.900, 76.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Cytochrome c family protein


Mass: 34954.703 Da / Num. of mol.: 1 / Fragment: unp residues 26-343
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter sulfurreducens (bacteria) / Strain: PCA / Gene: GSU1996 / Production host: Escherichia coli (E. coli) / Strain (production host): JCB7123 / References: UniProt: Q74BP5
#2: Chemical
ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 6.2 Å3/Da / Density % sol: 80.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.5 M ammonium sulfate, 2.5 M NaCl, 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: 1.5498 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Dec 2, 2003
RadiationMonochromator: monochromatic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5498 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 26822 / Num. obs: 26822 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 18.4
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2565 / % possible all: 91.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXDphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 3.2→20 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1762333.25 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.298 1624 6.5 %RANDOM
Rwork0.266 ---
obs0.266 25092 90.9 %-
all-25092 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 77.4073 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 90.8 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.71 Å0.6 Å
Luzzati d res low-5 Å
Luzzati sigma a1.02 Å0.94 Å
Refinement stepCycle: LAST / Resolution: 3.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2224 0 516 9 2749
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg4.1
X-RAY DIFFRACTIONc_dihedral_angle_d26.1
X-RAY DIFFRACTIONc_improper_angle_d3.1
X-RAY DIFFRACTIONc_mcbond_it1.551.5
X-RAY DIFFRACTIONc_mcangle_it2.832
X-RAY DIFFRACTIONc_scbond_it2.252
X-RAY DIFFRACTIONc_scangle_it3.182.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 3.2→3.4 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.469 221 6.3 %
Rwork0.431 3313 -
obs-3313 76.9 %
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 DIFFRACTION4cis_peptide.param

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