[English] 日本語
Yorodumi
- PDB-1ggh: CRYSTAL STRUCTURE OF CATALASE HPII FROM ESCHERICHIA COLI, HIS128A... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ggh
TitleCRYSTAL STRUCTURE OF CATALASE HPII FROM ESCHERICHIA COLI, HIS128ALA VARIANT.
ComponentsCATALASE HPII
KeywordsOXIDOREDUCTASE / BETA BARREL / ALPHA HELICAL DOMAIN / FLAVODOXIN LIKE DOMAIN
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 / cytoplasm / cytosol
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 / Resolution: 2.15 Å
AuthorsMelik-Adamyan, W.R. / Bravo, J. / Carpena, X. / Switala, J. / Mate, M.J. / Fita, I. / Loewen, P.C.
Citation
Journal: Proteins / Year: 2001
Title: Substrate flow in catalases deduced from the crystal structures of active site variants of HPII from Escherichia coli.
Authors: Melik-Adamyan, W. / Bravo, J. / Carpena, X. / Switala, J. / Mate, M.J. / Fita, I. / Loewen, P.C.
#1: Journal: Structure / Year: 1995
Title: Crystal Structure of Catalase HPII from Escherichia coli
Authors: Bravo, J. / Verdaguer, N. / Tormo, J. / Betzel, C. / Switala, J. / Loewen, P.C. / Fita, I.
#2: Journal: PROTEINS: STRUCT.,FUNCT.,GENET. / Year: 1999
Title: Structure of Catalase Hpii from Escherichia Coli at 1.9 A Resolution
Authors: Bravo, J. / Mate, M.J. / Schneider, T. / Switala, J. / Wilson, K. / Loewen, P.C. / Fita, I.
History
DepositionAug 21, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 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 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
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)339,2838
Polymers336,8184
Non-polymers2,4664
Water50,1902786
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area58590 Å2
ΔGint-274 kcal/mol
Surface area78040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.040, 132.340, 121.200
Angle α, β, γ (deg.)90.00, 109.63, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
CATALASE HPII


Mass: 84204.375 Da / Num. of mol.: 4 / Mutation: H128A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PH128A / Production host: Escherichia coli (E. coli) / 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.: 2786 / 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: 2.09 Å3/Da / Density % sol: 41.01 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 9
Details: PEG 3350, LiCl, Tris-HCl, pH 9.0, vapor diffusion/hanging drop, temperature 297.0K
Crystal grow
*PLUS
pH: 9 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
215-17 %PEG33501reservoir
31.6-1.5 M1reservoirLiCl
40.1 MTris-HCl1reservoir

-
Data collection

DiffractionMean temperature: 120 K
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.15→14.96 Å / Num. all: 149981 / Num. obs: 143588 / % possible obs: 95.9 % / Biso Wilson estimate: 19.4 Å2
Reflection shellResolution: 2.15→2.21 Å / Num. unique all: 11135 / % possible all: 93.3
Reflection
*PLUS
Rmerge(I) obs: 0.105
Reflection shell
*PLUS
% possible obs: 93.3 % / Num. unique obs: 11135 / Rmerge(I) obs: 0.264

-
Processing

Software
NameClassification
CCP4model building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementResolution: 2.15→87.65 Å / Stereochemistry target values: CCP4, protin_jp.idl
Details: REFMAC, WEIGHT MATRIX 0.2. X-Plor was also used during refinement
RfactorNum. reflection% reflection
Rfree0.206 7176 -
Rwork0.15 --
obs0.161 136412 95.8 %
all-142446 -
Refinement stepCycle: LAST / Resolution: 2.15→87.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22964 0 172 2786 25922
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.008
X-RAY DIFFRACTIONp_angle_d0.027
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.15
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_plane_restr0.019
X-RAY DIFFRACTIONp_chiral_restr0.11
LS refinement shell
*PLUS
Rfactor Rfree: 0.228 / Rfactor obs: 0.171

+
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