[English] 日本語
Yorodumi
- PDB-3o5c: Cytochrome c Peroxidase BccP of Shewanella oneidensis -

+
Open data


ID or keywords:

Loading...

-
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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more