[English] 日本語
Yorodumi
- PDB-1h6n: Formation of a tyrosyl radical intermediate in Proteus mirabilis ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1h6n
TitleFormation of a tyrosyl radical intermediate in Proteus mirabilis catalase by directed mutagenesis and consequences for nucleotide reactivity
ComponentsCATALASE
KeywordsOXIDOREDUCTASE (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 active site / Catalase proximal active site signature. / Catalase immune-responsive domain ...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 active site / Catalase proximal active site signature. / Catalase immune-responsive domain / Catalase-related immune-responsive / 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: 2.11 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: 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.
#2: 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.
#3: 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.
#4: 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.
History
DepositionJun 20, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 3, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 27, 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_biol / struct_conn
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp ..._exptl_crystal_grow.method / _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 1.4Dec 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
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 10-STRANDED BARREL THIS IS REPRESENTED BY A 11-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CATALASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5144
Polymers55,7421
Non-polymers7723
Water5,855325
1
A: CATALASE
hetero molecules

A: CATALASE
hetero molecules

A: CATALASE
hetero molecules

A: CATALASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,05616
Polymers222,9694
Non-polymers3,08612
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation4_655-x+1,-y,z1
crystal symmetry operation11_655-x+y+1,y,-z1
MethodPQS
Unit cell
Length a, b, c (Å)109.900, 109.900, 249.780
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-2041-

HOH

-
Components

#1: Protein CATALASE


Mass: 55742.348 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: METHIONINE SULFONE IN POSITION 53 TYROSINE 337 LACKS 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.: 325 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A ENGINEERED MUTATION PHE194TYR CONVERSION OF HYDROGEN PEROXIDE IN WATER AND OXYGEN PROTECTS ...CHAIN A ENGINEERED MUTATION PHE194TYR CONVERSION OF HYDROGEN PEROXIDE IN WATER AND OXYGEN PROTECTS CELLS FROM THE TOXIC EFFECTS OF HYDROGEN PEROXIDE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.89 Å3/Da / Density % sol: 67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.3 / Details: HANGING DROP AT 4 C, pH 7.30

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9574
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9574 Å / Relative weight: 1
ReflectionResolution: 2.11→29.67 Å / Num. obs: 51085 / % possible obs: 97.9 % / Observed criterion σ(I): 3 / Redundancy: 4.46 % / Biso Wilson estimate: 28.4 Å2 / Rsym value: 0.072
Reflection shellResolution: 2.11→2.24 Å / Rsym value: 0.22 / % possible all: 97.5

-
Processing

Software
NameVersionClassification
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CAE

1cae
PDB Unreleased entry


Resolution: 2.11→29.67 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2885037.81 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: AMINO ACIDS 358 - 362 ARE POORLY VISIBLE IN THE ELECTRON DENSITY MAP
RfactorNum. reflection% reflectionSelection details
Rfree0.236 2554 5 %RANDOM
Rwork0.22 ---
obs0.22 51085 97.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.2996 Å2 / ksol: 0.344736 e/Å3
Displacement parametersBiso mean: 50.5 Å2
Baniso -1Baniso -2Baniso -3
1-11.98 Å24.4 Å20 Å2
2--11.98 Å20 Å2
3----23.96 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.11→29.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3871 0 52 325 4248
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_d23.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.33
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.541.5
X-RAY DIFFRACTIONc_mcangle_it2.452
X-RAY DIFFRACTIONc_scbond_it0.422
X-RAY DIFFRACTIONc_scangle_it0.742.5
LS refinement shellResolution: 2.11→2.24 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.347 414 5 %
Rwork0.353 7868 -
obs--97.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_PARAM.VER9PROTEIN_VER9.TOP
X-RAY DIFFRACTION2HEM_XPLOR_PAR.TXTHEM_XPLOR_TOP.TXT
X-RAY DIFFRACTION3WATER_PARAM.VER9WATER_VER9.TOP
X-RAY DIFFRACTION4IONS.PARAMIONS.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://pdbjlvh1.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