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- PDB-3o5c: Cytochrome c Peroxidase BccP of Shewanella oneidensis -

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Basic information

Entry
Database: PDB / ID: 3o5c
TitleCytochrome c Peroxidase BccP of Shewanella oneidensis
ComponentsCytochrome c551 peroxidase
KeywordsOXIDOREDUCTASE / Diheme cytochrome / Hydrogen Peroxide
Function / homology
Function and homology information


cytochrome-c peroxidase / cytochrome-c peroxidase activity / 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
(R,R)-2,3-BUTANEDIOL / PROTOPORPHYRIN IX CONTAINING FE / Diheme cytochrome c5 peroxidase CcpA
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSeidel, J. / Einsle, O.
CitationJournal: Appl.Environ.Microbiol. / Year: 2011
Title: Investigation of the Electron Transport Chain to and the Catalytic Activity of the Diheme Cytochrome c Peroxidase CcpA of Shewanella oneidensis.
Authors: Schutz, B. / Seidel, J. / Sturm, G. / Einsle, O. / Gescher, J.
History
DepositionJul 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2011Group: Database references
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_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_asym_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_asym_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_asym_id / _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_asym_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_ref_seq_dif.details / _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 c551 peroxidase
B: Cytochrome c551 peroxidase
C: Cytochrome c551 peroxidase
D: Cytochrome c551 peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,23717
Polymers140,0554
Non-polymers5,18213
Water23,5641308
1
A: Cytochrome c551 peroxidase
B: Cytochrome c551 peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,5748
Polymers70,0272
Non-polymers2,5466
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8930 Å2
ΔGint-156 kcal/mol
Surface area23180 Å2
MethodPISA
2
C: Cytochrome c551 peroxidase
D: Cytochrome c551 peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,6649
Polymers70,0272
Non-polymers2,6367
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9230 Å2
ΔGint-151 kcal/mol
Surface area23130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.840, 81.220, 85.920
Angle α, β, γ (deg.)113.96, 102.10, 90.01
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Cytochrome c551 peroxidase


Mass: 35013.746 Da / Num. of mol.: 4 / Fragment: UNP residues 23-333
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Gene: ccpA, SO_2178 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8EF24
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1308 / 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: 2.25 Å3/Da / Density % sol: 45.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5
Details: reduced with sodium dithionite, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.93 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Nov 28, 2009
RadiationMonochromator: Ge(111) triangular bent compressing 7 Fankuchen cut
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.8→40.5 Å / Num. all: 200196 / Num. obs: 106139 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 10.7 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.113 / Net I/σ(I): 6.7

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3HQ6

3hq6


Resolution: 1.8→40.5 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.886 / SU B: 7.322 / SU ML: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25695 5345 5 %RANDOM
Rwork0.19759 ---
all0.20055 200196 --
obs-100779 93.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.729 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20.01 Å20.04 Å2
2---0.05 Å20.01 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.8→40.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9419 0 354 1308 11081
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02210098
X-RAY DIFFRACTIONr_bond_other_d0.0010.026744
X-RAY DIFFRACTIONr_angle_refined_deg1.2322.07513830
X-RAY DIFFRACTIONr_angle_other_deg0.892316542
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.81451233
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.83325.208409
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.672151613
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.1931532
X-RAY DIFFRACTIONr_chiral_restr0.0680.21452
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02111155
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021813
X-RAY DIFFRACTIONr_mcbond_it0.4211.56151
X-RAY DIFFRACTIONr_mcbond_other0.1131.52458
X-RAY DIFFRACTIONr_mcangle_it0.7129952
X-RAY DIFFRACTIONr_scbond_it1.27433947
X-RAY DIFFRACTIONr_scangle_it1.94.53875
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 364 -
Rwork0.267 6798 -
obs-100779 85.9 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.14380.0415-0.3350.7543-0.16621.32430.0077-0.1115-0.08680.0713-0.03070.01780.02930.09360.02310.0119-0.0005-0.00590.01450.00640.0233-0.11650.3163-1.8113
20.7118-0.0014-0.50440.40860.01091.60310.03790.14080.1062-0.06710.004-0.0005-0.1315-0.0532-0.04190.03420.0111-0.00230.03980.00940.0369-12.307517.9342-25.804
31.3408-0.01640.37820.6495-0.07391.38990.00230.20620.1365-0.0948-0.0283-0.0021-0.0210.11040.0260.01770.00130.00810.03550.01670.032425.2666-29.3923-8.8128
40.7260.10780.48560.43810.19711.64260.0449-0.1256-0.09710.0978-0.00310.01520.1473-0.0631-0.04180.0426-0.01090.00410.02950.00790.042412.8987-46.168915.8828
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999
3X-RAY DIFFRACTION3C-10 - 9999
4X-RAY DIFFRACTION4D-10 - 9999

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