[English] 日本語
Yorodumi
- PDB-1h5c: X-ray induced reduction of horseradish peroxidase C1A Compound II... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1h5c
TitleX-ray induced reduction of horseradish peroxidase C1A Compound III (100-200% dose)
ComponentsPEROXIDASE C1A
KeywordsOXIDOREDUCTASE / PEROXIDASE / HORSERADISH / COMPOUND III / OXYPEROXIDASE / X-RAY INDUCED REDUCTION
Function / homology
Function and homology information


peroxidase / lactoperoxidase activity / vacuole / hydrogen peroxide catabolic process / response to oxidative stress / heme binding / extracellular region / metal ion binding
Similarity search - Function
Plant peroxidase / Secretory peroxidase / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. / Haem peroxidase ...Plant peroxidase / Secretory peroxidase / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. / Haem peroxidase / Peroxidase / Peroxidase; domain 1 / Peroxidases proximal heme-ligand signature. / Haem peroxidase superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / PROTOPORPHYRIN IX CONTAINING FE / Peroxidase C1A
Similarity search - Component
Biological speciesARMORACIA RUSTICANA (horseradish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.62 Å
AuthorsBerglund, G.I. / Carlsson, G.H. / Hajdu, J. / Smith, A.T. / Szoke, H. / Henriksen, A.
Citation
Journal: Nature / Year: 2002
Title: The Catalytic Pathway of Horseradish Peroxidase at High Resolution
Authors: Berglund, G.I. / Carlsson, G.H. / Smith, A.T. / Szoke, H. / Henriksen, A. / Hajdu, J.
#1: Journal: J.Biol.Chem. / Year: 1999
Title: The Structures of the Horseradish Peroxidase C-Ferulic Acid Complex and the Ternary Complex with Cyanide Suggest How Peroxidases Oxidize Small Phenolic Substrates
Authors: Henriksen, A. / Smith, A.T. / Gajhede, M.
#2: Journal: Nat.Struct.Biol. / Year: 1997
Title: Crystal Structure of Horseradish Peroxidase C at 2.15 A Resolution
Authors: Gajhede, M. / Schuller, D.J. / Henriksen, A. / Smith, A.T. / Poulos, T.L.
#3: Journal: J.Biol.Chem. / Year: 1990
Title: Expression of a Synthetic Gene for Horseradish Peroxidase C in Escherichia Coli and Folding and Activation of the Recombinant Enzyme with Ca2+ and Heme
Authors: Smith, A.T. / Santama, N. / Dacey, S. / Edwards, M. / Bray, R.C. / Thorneley, R.N. / Burke, J.F.
History
DepositionMay 21, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 18, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / 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_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _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_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: PEROXIDASE C1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7045
Polymers33,9481
Non-polymers7564
Water7,566420
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)40.206, 67.049, 117.146
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein PEROXIDASE C1A


Mass: 33948.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARMORACIA RUSTICANA (horseradish) / Description: SYNTHETIC GENE / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P00433, peroxidase
#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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 420 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE SWS ENTRY INCLUDES N-TERM AND C-TERM SIGNAL PEPTIDES.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.9 %
Description: X-RAY EXPOSURE CORRESPONDS TO 100-200% DOSE (SEE JRNL). AN X-RAY DOSE OF 0-100% REPRESENTS THE DOSE REQUIRED FOR THE COLLECTION OF A COMPLETE DATA SET FROM ONE CRYSTAL. STARTING MODEL ...Description: X-RAY EXPOSURE CORRESPONDS TO 100-200% DOSE (SEE JRNL). AN X-RAY DOSE OF 0-100% REPRESENTS THE DOSE REQUIRED FOR THE COLLECTION OF A COMPLETE DATA SET FROM ONE CRYSTAL. STARTING MODEL FOR RIGID-BODY REFINEMENT WAS PDB ENTRY 7ATJ
Crystal growpH: 6.5
Details: 20% (W/V) PEG 4000, 0.2 M CALCIUM ACETATE, 0.1 M CACODYLATE BUFFER, PH 6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 15, 2000 / Details: MULTILAYER
RadiationMonochromator: DIAMOND (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.62→34.5 Å / Num. obs: 41017 / % possible obs: 99.8 % / Redundancy: 3.84 % / Biso Wilson estimate: 16.1 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 15.5
Reflection shellResolution: 1.62→1.66 Å / Rmerge(I) obs: 0.291 / Mean I/σ(I) obs: 5.3 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: OTHER / Resolution: 1.62→34.48 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1355500.18 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: SER 306 WAS THE LAST RESIDUE SEEN IN THE ELECTRON DENSITY MAP THE FOLLOWING RESIDUES HAVE BEEN MODELLED IN DUAL CONFORMATIONS: 15,91,151,161,219,240,249,264, 286
RfactorNum. reflection% reflectionSelection details
Rfree0.198 2058 5 %RANDOM
Rwork0.178 ---
obs0.178 41017 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.0391 Å2 / ksol: 0.350548 e/Å3
Displacement parametersBiso mean: 14.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å20 Å20 Å2
2--2.13 Å20 Å2
3----1.68 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.07 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 1.62→34.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2369 0 49 420 2838
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.08
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.911.5
X-RAY DIFFRACTIONc_mcangle_it1.322
X-RAY DIFFRACTIONc_scbond_it1.592
X-RAY DIFFRACTIONc_scangle_it2.252.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.253 256 4.7 %
Rwork0.221 5157 -
obs--77.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

+
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