[English] 日本語
Yorodumi
- PDB-3r99: Joint Neutron and X-ray structure of Cytochrome c peroxidase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3r99
TitleJoint Neutron and X-ray structure of Cytochrome c peroxidase
ComponentsCytochrome c peroxidase
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


cytochrome-c peroxidase / cytochrome-c peroxidase activity / peroxidase activity / response to reactive oxygen species / hydrogen peroxide catabolic process / mitochondrial intermembrane space / cellular response to oxidative stress / mitochondrial matrix / heme binding / mitochondrion / metal ion binding
Similarity search - Function
Class I peroxidase / Heme-binding peroxidase Ccp1-like / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Peroxidase; domain 1 / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. ...Class I peroxidase / Heme-binding peroxidase Ccp1-like / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Peroxidase; domain 1 / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. / Haem peroxidase / Peroxidase / Peroxidases proximal heme-ligand signature. / Haem peroxidase superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DEUTERATED WATER / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome c peroxidase, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodNEUTRON DIFFRACTION / X-RAY DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBlakeley, M.P. / Fisher, S.J. / Gumiero, A. / Moody, P.C.E. / Raven, E.L.
CitationJournal: To be Published
Title: Hydrogen bonds in heme peroxidases: a combined X-ray and neutron study of cytochrome c peroxidase
Authors: Gumiero, A. / Blakeley, M.P. / Metcalfe, C.L. / Murphy, E.J. / Raven, E.L. / Moody, P.C.E.
History
DepositionMar 25, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2May 16, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site ..._diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.source / _diffrn_source.type
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_conn.ptnr2_label_seq_id / _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 c peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0872
Polymers33,4701
Non-polymers6161
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.547, 76.655, 107.078
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Cytochrome c peroxidase / / CCP


Mass: 33470.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Genus: CCP1, CCP, CPO, YKR066C / Production host: Escherichia coli (E. coli) / References: UniProt: P00431, cytochrome-c peroxidase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-DOD / water / Heavy water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: D2O

-
Experimental details

-
Experiment

Experiment
MethodNumber of used crystals
NEUTRON DIFFRACTION1
X-RAY DIFFRACTION2

-
Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 61.08 %
Crystal growTemperature: 298 K / Method: microdialysis / pH: 6
Details: 50mM potassium phosphate, 30% MPD, pH 6.0(in D2O), MICRODIALYSIS, temperature 298K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12981
22981
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
NUCLEAR REACTORILL LADI III13.2-4.2
ROTATING ANODERIGAKU21.5418
Detector
TypeIDDetectorDate
1IMAGE PLATEJun 23, 2009
RIGAKU RAXIS IV2IMAGE PLATEApr 13, 2009
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Multilayer Ni-TiLAUEMneutron1
2XenocsSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
13.21
24.21
31.54181
Reflection

Entry-ID: 3R99

Resolution (Å)Num. allNum. obs% possible obs (%)Observed criterion σ(F)Observed criterion σ(I)Redundancy (%)Biso Wilson estimate (Å2)Rmerge(I) obsDiffraction-IDNet I/σ(I)
2.4-53.55169061290076.3004.629.960.16817.8
2.1-43.8932290089.92
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
2.4-2.532.50.19451358156.6
2.1-2.17284

-
Processing

Software
NameVersionClassification
QLDdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.4_486)refinement
LAUEGENdata reduction
SCALAdata scaling
PHENIXphasing
Refinement

Baniso 13: -0 Å2 / Baniso 23: 0 Å2 / Method to determine structure: MOLECULAR REPLACEMENT / Stereochemistry target values: ML / Solvent model: FLAT BULK SOLVENT MODEL

Resolution (Å)Refine-IDBaniso 11 (Å2)Baniso 12 (Å2)Baniso 22 (Å2)Baniso 33 (Å2)Rfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection obs% reflection Rfree (%)% reflection obs (%)Diffraction-IDσ(F)Shrinkage radii (Å)VDW probe radii (Å)Bsol (Å2)ksol (e/Å3)Biso max (Å2)Biso mean (Å2)Biso min (Å2)Num. reflection RworkOccupancy maxOccupancy minSU MLPhase error
2.4-53.539NEUTRON DIFFRACTION-5.956-0-1.5485-11.86620.24990.20710.21151290129001075.01100.770.9200.404
2.1-43.893X-RAY DIFFRACTION1.330105.3682-9.85480.20270.16620.169822922290010.0189.8921.360.650.8400.38995.1432.468511.9120608100.319.57
Refinement stepCycle: LAST / Resolution: 2.4→53.539 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2367 0 43 174 2584
Refine LS restraints
Refine-IDTypeDev idealNumber
NEUTRON DIFFRACTIONf_bond_d0.0165617
NEUTRON DIFFRACTIONf_angle_d1.6499671
NEUTRON DIFFRACTIONf_chiral_restr0.173332
NEUTRON DIFFRACTIONf_plane_restr0.0081077
NEUTRON DIFFRACTIONf_dihedral_angle_d19.9961496
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-IDNum. reflection allTotal num. of bins used% reflection obs (%)
2.4-2.49610.36751020.3145919NEUTRON DIFFRACTION1021955
2.4961-2.60970.32531100.2827990NEUTRON DIFFRACTION1100959
2.6097-2.74730.29941180.2541052NEUTRON DIFFRACTION1170962
2.7473-2.91940.30131250.23181120NEUTRON DIFFRACTION1245967
2.9194-3.14480.23921370.21851241NEUTRON DIFFRACTION1378972
3.1448-3.46120.25851520.18811381NEUTRON DIFFRACTION1533980
3.4612-3.96190.21211740.17231569NEUTRON DIFFRACTION1743991
3.9619-4.99110.20061810.16661611NEUTRON DIFFRACTION1792993
4.9911-53.55230.23081910.19311727NEUTRON DIFFRACTION1918993
2.1-2.17510.30892110.24891899X-RAY DIFFRACTION21101084
2.1751-2.26220.29892110.21321895X-RAY DIFFRACTION21061084
2.2622-2.36510.22892120.18291908X-RAY DIFFRACTION21201085
2.3651-2.48980.23482110.18131910X-RAY DIFFRACTION21211084
2.4898-2.64580.24252130.18631915X-RAY DIFFRACTION21281085
2.6458-2.850.2312220.1781982X-RAY DIFFRACTION22041087
2.85-3.13670.20112400.17732162X-RAY DIFFRACTION24021095
3.1367-3.59040.22052480.1692242X-RAY DIFFRACTION24901097
3.5904-4.52290.15232540.13152295X-RAY DIFFRACTION25491098
4.5229-43.90250.17292700.15312400X-RAY DIFFRACTION26701098

+
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://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