[English] 日本語
Yorodumi
- PDB-1e93: High resolution structure and biochemical properties of a recombi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1.0E+93
TitleHigh resolution structure and biochemical properties of a recombinant catalase depleted in iron
ComponentsCATALASE
KeywordsOXIDOREDUCTASE / OXIDOREDUCTASE (H2O2 ACCEPTOR) / PEROXIDASE / IRON / HEM / HYDROGEN PEROXIDE / NADP
Function / homology
Function and homology information


catalase / catalase activity / hydrogen peroxide catabolic process / response to hydrogen peroxide / heme binding / metal ion binding / cytoplasm
Similarity search - Function
Catalase, clade 3 / Catalase, mono-functional, haem-containing, clades 1 and 3 / 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, clade 3 / Catalase, mono-functional, haem-containing, clades 1 and 3 / 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 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / PROTOPORPHYRIN IX CONTAINING FE / Catalase
Similarity search - Component
Biological speciesPROTEUS MIRABILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsAndreoletti, P. / Sainz, G. / Jaquinod, M. / Gagnon, J. / Jouve, H.M.
Citation
Journal: Proteins: Struct.,Funct., Genet. / Year: 2003
Title: High-Resolution Structure and Biochemical Properties of a Recombinant Proteus Mirabilis Catalase Depleted in Iron.
Authors: Andreoletti, P. / Sainz, G. / Jaquinod, M. / Gagnon, J. / Jouve, H.M.
#1: Journal: J.Mol.Biol. / Year: 1995
Title: Crystal Structure of Proteus Mirabilis Pr Catalase with and without Bound Nadph
Authors: Gouet, P. / Jouve, H.M. / Dideberg, O.
#2: Journal: J.Mol.Biol. / Year: 1991
Title: Crystallization and Crystal Packing of Proteus Mirabilis Pr Catalase
Authors: Jouve, H.M. / Gouet, P. / Boudjada, N. / Buisson, G. / Kahn, R. / Duee, E.
#3: Journal: Acta Crystallogr.,Sect.B / Year: 1986
Title: The Refined Structure of Beef Liver Catalase at 2.5 Angstroms Resolution
Authors: Fita, I. / Silva, A.M. / Murthy, M.R.N. / Rossmann, M.G.
#4: Journal: Nat.Struct.Biol. / Year: 1996
Title: Ferryl Intermediates of Catalase Captured by Time-Resolved Weissenberg Crystallography and Uv-Vis Spectroscopy
Authors: Gouet, P. / Jouve, H.M. / Williams, P.A. / Andersson, I. / Andreoletti, P. / Nussaume, L. / Hajdu, J.
History
DepositionOct 5, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 13, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval ..._exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_seq_map_depositor_info
Item: _exptl_crystal_grow.method / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CATALASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4984
Polymers55,7261
Non-polymers7723
Water11,061614
1
A: CATALASE
hetero molecules

A: CATALASE
hetero molecules

A: CATALASE
hetero molecules

A: CATALASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,99216
Polymers222,9064
Non-polymers3,08612
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
crystal symmetry operation11_655-x+y+1,y,-z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area45920 Å2
ΔGint-298.58 kcal/mol
Surface area56960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.572, 108.572, 248.760
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-2066-

HOH

21A-2073-

HOH

31A-2151-

HOH

41A-2159-

HOH

51A-2188-

HOH

61A-2531-

HOH

-
Components

#1: Protein CATALASE


Mass: 55726.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: METHIONINE SULFONE IN POSITION 53 TYROSINE 337 LACK THE HYDROXYL HYDROGEN
Source: (gene. exp.) PROTEUS MIRABILIS (bacteria) / Gene: KATA / Plasmid: PALTER-CAT / Gene (production host): KATA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109 DE3 / References: UniProt: P42321, catalase
#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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 614 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCONVERSION OF HYDROGEN PEROXIDE IN WATER AND OXYGEN PROTECTS CELLS FROM THE TOXIC EFFECTS OF ...CONVERSION OF HYDROGEN PEROXIDE IN WATER AND OXYGEN PROTECTS CELLS FROM THE TOXIC EFFECTS OF HYDROGEN PEROXIDE.
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.82 Å3/Da / Density % sol: 63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.3 / Details: HANGING DROP AT 4 DEGREE C, pH 7.30
Crystal grow
*PLUS
Temperature: 4-5 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Details: drop was mixed with an equal volume of reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
154 mg/mlprotein1drop
2100 mMTris-HCl1drop
35 %(v/v)glycerol1drop
4100 mMTris-HCl1reservoir
52 Mammonium sulfate1reservoir
650 mM1reservoirKCl

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9574
DetectorDetector: IMAGE PLATE / Date: Jul 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9574 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 58298 / % possible obs: 97.7 % / Observed criterion σ(I): 3 / Redundancy: 4.46 % / Biso Wilson estimate: 12.9 Å2 / Rsym value: 0.072
Reflection shellResolution: 2→2.05 Å / Rsym value: 0.22 / % possible all: 94.6
Reflection
*PLUS
% possible obs: 97.8 % / Redundancy: 5.7 % / Num. measured all: 332299 / Rmerge(I) obs: 0.072
Reflection shell
*PLUS
% possible obs: 94.6 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.22

-
Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CAE

1cae
PDB Unreleased entry


Resolution: 2→14.95 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3292293.35 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: AMINO ACIDS 358 - 362 ARE POORLY VISIBLE IN THE ELECTRON DENSITY MAP THE 5 C-TERMINAL RESIDUES WAS NOT SEEN IN THE DENSITY MAPS
RfactorNum. reflection% reflectionSelection details
Rfree0.215 2931 5.1 %RANDOM
Rwork0.199 ---
obs0.199 57838 97.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.6112 Å2 / ksol: 0.333625 e/Å3
Displacement parametersBiso mean: 25.9 Å2
Baniso -1Baniso -2Baniso -3
1-7.32 Å20.22 Å20 Å2
2--7.32 Å20 Å2
3----14.63 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2→14.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3870 0 52 614 4536
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.26
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.561.5
X-RAY DIFFRACTIONc_mcangle_it0.772
X-RAY DIFFRACTIONc_scbond_it0.962
X-RAY DIFFRACTIONc_scangle_it1.22.5
LS refinement shellResolution: 2→2.12 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.276 464 5.1 %
Rwork0.251 8676 -
obs--94.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_PARAM.VER1PROTEIN_VER1.TOP
X-RAY DIFFRACTION2HEM_XPLOR_PAR.TXTHEM_XPLOR_TOP.TXT
X-RAY DIFFRACTION3WATER_PARAM.VER1WATER_VER1.TOP
X-RAY DIFFRACTION4IONS.PARAMIONS.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 15 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.26

+
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