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- PDB-4rlr: Structure of monoheme cytochrome PccH from Geobacter sulfurreducens -

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Basic information

Entry
Database: PDB / ID: 4rlr
TitleStructure of monoheme cytochrome PccH from Geobacter sulfurreducens
ComponentsCytochrome c, 1 heme-binding site
KeywordsELECTRON TRANSPORT / novel monoheme cytochrome / electrode
Function / homology
Function and homology information


electron transfer activity / heme binding / metal ion binding
Similarity search - Function
Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
ACETATE ION / CACODYLATE ION / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome c, 1 heme-binding site
Similarity search - Component
Biological speciesGeobacter sulfurreducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.002 Å
AuthorsPokkuluri, P.R. / Salgueiro, C.A.
CitationJournal: Febs J. / Year: 2015
Title: The structure of PccH from Geobacter sulfurreducens - a novel low reduction potential monoheme cytochrome essential for accepting electrons from an electrode.
Authors: Dantas, J.M. / Campelo, L.M. / Duke, N.E. / Salgueiro, C.A. / Pokkuluri, P.R.
History
DepositionOct 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_atom_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.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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_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

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Assembly

Deposited unit
A: Cytochrome c, 1 heme-binding site
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8717
Polymers14,8621
Non-polymers1,0096
Water3,189177
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Cytochrome c, 1 heme-binding site
hetero molecules

A: Cytochrome c, 1 heme-binding site
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,74114
Polymers29,7242
Non-polymers2,01712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area5450 Å2
ΔGint-260 kcal/mol
Surface area12040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.311, 63.311, 78.682
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-425-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cytochrome c, 1 heme-binding site


Mass: 14861.936 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter sulfurreducens (bacteria) / Gene: GSU3274 / Production host: Escherichia coli (E. coli) / References: UniProt: Q747J2

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Non-polymers , 5 types, 183 molecules

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


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.65 Å3/Da / Density % sol: 53.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Crystal screen #45 (0.2 M zinc acetate, 0.1 M sodium cacodylate pH 6.5, 18% PEG8000) diluted 4:1 by water, 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: 1.72202, 0.97927
DetectorDetector: CCD / Date: Aug 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.722021
20.979271
ReflectionResolution: 2→100 Å / Num. all: 11316 / Num. obs: 11316 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 12 % / Biso Wilson estimate: 25.4 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 46
Reflection shellResolution: 2→2.02 Å / Redundancy: 11 % / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 4.9 / Num. unique all: 296 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000phasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.002→29.552 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.52 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2316 897 4.45 %random
Rwork0.1899 ---
obs0.1918 20138 97.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.002→29.552 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms988 0 55 177 1220
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.021092
X-RAY DIFFRACTIONf_angle_d1.4921497
X-RAY DIFFRACTIONf_dihedral_angle_d17.309363
X-RAY DIFFRACTIONf_chiral_restr0.083144
X-RAY DIFFRACTIONf_plane_restr0.007184
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0025-2.12790.25321550.21533280X-RAY DIFFRACTION100
2.1279-2.29210.39171340.32722913X-RAY DIFFRACTION89
2.2921-2.52270.29051490.21263260X-RAY DIFFRACTION100
2.5227-2.88750.27281540.19153274X-RAY DIFFRACTION100
2.8875-3.63690.21061610.17563255X-RAY DIFFRACTION100
3.6369-29.55490.16311440.15143259X-RAY DIFFRACTION99

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