[English] 日本語
Yorodumi
- PDB-1p7y: Crystal structure of the D181A variant of catalase HPII from E. coli -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1p7y
TitleCrystal structure of the D181A variant of catalase HPII from E. coli
ComponentsCatalase HPII
KeywordsOXIDOREDUCTASE / catalase / beta barrel / channel
Function / homology
Function and homology information


catalase / catalase activity / hyperosmotic response / hydrogen peroxide catabolic process / response to oxidative stress / iron ion binding / heme binding / DNA damage response / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Catalase, four-helical domain / C-terminal domain found in long catalases / Catalase, mono-functional, haem-containing, clade 2 / Large catalase, C-terminal domain / Catalase, mono-functional, haem-containing, clade 2, helical domain / Hemocyanin, N-terminal domain / Catalase HpII, Chain A, domain 1 / Catalase core domain / Catalase haem-binding site / Catalase proximal heme-ligand signature. ...Catalase, four-helical domain / C-terminal domain found in long catalases / Catalase, mono-functional, haem-containing, clade 2 / Large catalase, C-terminal domain / Catalase, mono-functional, haem-containing, clade 2, helical domain / Hemocyanin, N-terminal domain / Catalase HpII, Chain A, domain 1 / Catalase core domain / Catalase haem-binding site / Catalase proximal heme-ligand signature. / Catalase / Catalase immune-responsive domain / Catalase-related immune-responsive / Catalase active site / Catalase proximal active site signature. / Catalase core domain / Catalase, mono-functional, haem-containing / Catalase / catalase family profile. / Catalase superfamily / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Up-down Bundle / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Catalase HPII
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsChelikani, P. / Carpena, X. / Fita, I. / Loewen, P.C.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: An electrical potential in the access channel of catalases enhances catalysis
Authors: Chelikani, P. / Carpena, X. / Fita, I. / Loewen, P.C.
History
DepositionMay 6, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Catalase HPII
B: Catalase HPII
C: Catalase HPII
D: Catalase HPII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)339,3768
Polymers336,9104
Non-polymers2,4664
Water49,8482767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area58340 Å2
ΔGint-272 kcal/mol
Surface area78150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.29, 132.86, 121.75
Angle α, β, γ (deg.)90.00, 109.4, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Catalase HPII / Hydroxyperoxidase II


Mass: 84227.438 Da / Num. of mol.: 4 / Mutation: D181A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: katE / Plasmid: pD181A / Production host: Escherichia coli (E. coli) / Strain (production host): UM255 / References: UniProt: P21179, catalase
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2767 / 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: 2.11 Å3/Da / Density % sol: 41.73 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9
Details: PEG 3350, LiCl, Tris, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
115-17 %PEG33501reservoir
21.6-1.7 M1reservoirLiCl
30.1 MTris1reservoirpH9.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9755 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 15, 2001
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9755 Å / Relative weight: 1
ReflectionResolution: 2.4→29.8 Å / Num. all: 105796 / Num. obs: 105796 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 30.7 Å2 / Rmerge(I) obs: 0.135 / Rsym value: 0.135 / Net I/σ(I): 9.8
Reflection shellResolution: 2.4→2.94 Å / Redundancy: 2.25 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 1.8 / Num. unique all: 7994 / Rsym value: 0.36 / % possible all: 88.8
Reflection
*PLUS
Num. obs: 105578
Reflection shell
*PLUS
Lowest resolution: 2.49 Å / % possible obs: 88.8 % / Num. unique obs: 7994

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1GGE

1gge


Resolution: 2.4→29.8 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.225 5332 -random
Rwork0.144 ---
all0.154 105578 --
obs0.149 105578 96.8 %-
Displacement parametersBiso mean: 26.2 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 2.4→29.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22988 0 172 2767 25927
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.012
X-RAY DIFFRACTIONr_angle_refined_deg2.4
X-RAY DIFFRACTIONr_gen_planes_refined0.024
LS refinement shellResolution: 2.4→2.94 Å
RfactorNum. reflection% reflection
Rfree0.278 415 -
Rwork0.187 --
obs-7994 88.8 %
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.012
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg2.4
LS refinement shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.49 Å

+
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