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- PDB-3oue: Structure of C-terminal hexaheme fragment of GSU1996 -

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Basic information

Entry
Database: PDB / ID: 3oue
TitleStructure of C-terminal hexaheme fragment of GSU1996
ComponentsCytochrome c family protein
KeywordsELECTRON TRANSPORT / multiheme cytochrome-c / electron transfer / Fe reduction / Geobacter sulfurreducens / cytochrome c7 (c3) fold
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 / MAD / Resolution: 2.15 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 c polymer
Authors: Pokkuluri, P.R. / Londer, Y.Y. / Duke, N.E. / Erickson, J. / Pessanha, M. / Salgueiro, C.A. / Schiffer, M.
History
DepositionSep 14, 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_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / 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 / _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)21,1929
Polymers17,2891
Non-polymers3,9038
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.800, 66.400, 94.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cytochrome c family protein


Mass: 17289.057 Da / Num. of mol.: 1
Fragment: C-terminal hexaheme fragment of GSU1996 (unp residues 186-343)
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.71 Å3/Da / Density % sol: 66.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: SaltRx-50: 1.8 M ammonium dihydrogen phosphate, 0.1 M sodium acetate, pH 4.6, 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: 1.033 / Wavelength: 1.74080, 1.73866, 1.69123, 1.78883
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Aug 25, 2003
RadiationMonochromator: MONOCHROMATIC / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.0331
21.74081
31.738661
41.691231
51.788831
ReflectionResolution: 2.15→50 Å / Num. obs: 24950 / % possible obs: 91.8 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 14.8 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 34
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.237 / Mean I/σ(I) obs: 5 / % possible all: 64.6

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.15→28.01 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 703271.17 / 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
Rfree0.251 2223 9.4 %RANDOM
Rwork0.221 ---
obs0.221 23755 88.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.03 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 47.5 Å2
Baniso -1Baniso -2Baniso -3
1-26.94 Å20 Å20 Å2
2---11.31 Å20 Å2
3----15.63 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.15→28.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1197 0 268 60 1525
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_deg3.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.56
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.471.5
X-RAY DIFFRACTIONc_mcangle_it2.532
X-RAY DIFFRACTIONc_scbond_it2.122
X-RAY DIFFRACTIONc_scangle_it3.092.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.15→2.28 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.296 244 8.8 %
Rwork0.268 2536 -
obs--62.3 %
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.PARAMION.TOP
X-RAY DIFFRACTION5ION.PARAM

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