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- PDB-3hq7: CcpA from G. sulfurreducens, G94K/K97Q/R100I variant -

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Basic information

Entry
Database: PDB / ID: 3hq7
TitleCcpA from G. sulfurreducens, G94K/K97Q/R100I variant
ComponentsCytochrome c551 peroxidase
KeywordsOXIDOREDUCTASE / Cytochrome c peroxidase / Peroxidase
Function / homology
Function and homology information


cytochrome-c peroxidase activity / periplasmic space / electron transfer activity / heme binding / metal ion binding
Similarity search - Function
Di-c-type haem protein, MauG/cytochrome c peroxidase / Di-haem cytochrome c peroxidase / Di-haem cytochrome c peroxidase / : / 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 ...Di-c-type haem protein, MauG/cytochrome c peroxidase / Di-haem cytochrome c peroxidase / Di-haem cytochrome c peroxidase / : / 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 peroxidase
Similarity search - Component
Biological speciesGeobacter sulfurreducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsHoffmann, M. / Seidel, J. / Einsle, O.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: CcpA from Geobacter sulfurreducens is a basic di-heme cytochrome c peroxidase.
Authors: Hoffmann, M. / Seidel, J. / Einsle, O.
History
DepositionJun 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome c551 peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2314
Polymers36,9581
Non-polymers1,2733
Water3,297183
1
A: Cytochrome c551 peroxidase
hetero molecules

A: Cytochrome c551 peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,4638
Polymers73,9172
Non-polymers2,5466
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area7830 Å2
ΔGint-144 kcal/mol
Surface area26450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.299, 99.353, 78.225
Angle α, β, γ (deg.)89.97, 89.98, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Cytochrome c551 peroxidase


Mass: 36958.273 Da / Num. of mol.: 1 / Mutation: G94K,K97Q,R100I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter sulfurreducens (bacteria) / Gene: ccpA, ccpA-2, GSU2813 / Production host: Escherichia coli (E. coli) / References: UniProt: Q749D0, cytochrome-c peroxidase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.88 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1.05 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 21, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 2.3→70 Å / Num. obs: 17841 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Redundancy: 15.2 % / Rsym value: 0.146 / Net I/σ(I): 15

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3HQ6

3hq6


Resolution: 2.31→70 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.893 / SU B: 8.196 / SU ML: 0.197 / Cross valid method: THROUGHOUT / ESU R: 0.304 / ESU R Free: 0.268 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29373 906 5.1 %RANDOM
Rwork0.20879 ---
obs0.2129 16870 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.489 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20 Å20 Å2
2--0.87 Å20 Å2
3----1.75 Å2
Refinement stepCycle: LAST / Resolution: 2.31→70 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2287 0 87 183 2557
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.0222441
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.7832.0833341
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.1795301
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.62624.94489
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.215380
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.764157
X-RAY DIFFRACTIONr_chiral_restr0.1740.2356
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021853
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2850.21245
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.320.21593
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.250.2184
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.3350.25
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.230.238
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1220.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5131.51575
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.43822434
X-RAY DIFFRACTIONr_scbond_it3.69931026
X-RAY DIFFRACTIONr_scangle_it5.1724.5903
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.31→2.365 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.404 62 -
Rwork0.302 1191 -
obs--97.13 %

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