[English] 日本語
Yorodumi
- PDB-1sj2: Crystal structure of Mycobacterium tuberculosis catalase-peroxidase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1sj2
TitleCrystal structure of Mycobacterium tuberculosis catalase-peroxidase
ComponentsPeroxidase/catalase T
KeywordsOXIDOREDUCTASE / HOMODIMER
Function / homology
Function and homology information


oxidoreductase activity, acting on a heme group of donors, nitrogenous group as acceptor / Tolerance of reactive oxygen produced by macrophages / catalase-peroxidase / cell wall / NADH binding / catalase activity / NADPH binding / positive regulation of DNA repair / peptidoglycan-based cell wall / hydrogen peroxide catabolic process ...oxidoreductase activity, acting on a heme group of donors, nitrogenous group as acceptor / Tolerance of reactive oxygen produced by macrophages / catalase-peroxidase / cell wall / NADH binding / catalase activity / NADPH binding / positive regulation of DNA repair / peptidoglycan-based cell wall / hydrogen peroxide catabolic process / peroxidase activity / cellular response to hydrogen peroxide / response to oxidative stress / response to antibiotic / heme binding / extracellular region / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Catalase-peroxidase haem / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Peroxidase; domain 1 / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. / Haem peroxidase ...Catalase-peroxidase haem / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Peroxidase; domain 1 / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. / Haem peroxidase / Peroxidase / Peroxidases proximal heme-ligand signature. / Haem peroxidase superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Catalase-peroxidase / Catalase-peroxidase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsBertrand, T. / Eady, N.A.J. / Jones, J.N. / Bodiguel, J. / Jesmin / Nagy, J.M. / Raven, E.L. / Jamart-Gregoire, B. / Brown, K.A.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Crystal Structure of Mycobacterium tuberculosis Catalase-Peroxidase.
Authors: Bertrand, T. / Eady, N.A.J. / Jones, J.N. / Jesmin / Nagy, J.M. / Jamart-Gregoire, B. / Raven, E.L. / Brown, K.A.
History
DepositionMar 2, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / 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_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_ref_seq_dif.details / _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/catalase T
B: Peroxidase/catalase T
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,91210
Polymers162,1262
Non-polymers1,7868
Water12,665703
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13370 Å2
ΔGint-99 kcal/mol
Surface area49850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.330, 150.330, 154.281
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
DetailsThe asymmetric unit contains two molecules but to actually regenerate the biological dimer one should apply the following transformation : -Y, -X, -Z

-
Components

#1: Protein Peroxidase/catalase T / Catalase-peroxidase T


Mass: 81063.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: KATG, RV1908C, MT1959, MTCY180.10 / Plasmid: pTrc99A / Production host: Escherichia coli (E. coli) / Strain (production host): UM255 / References: UniProt: Q08129, UniProt: P9WIE5*PLUS, catalase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 703 / 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: 2.78 Å3/Da / Density % sol: 55.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 3350, Sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 11, 2003
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.41→23.71 Å / Num. all: 68475 / Num. obs: 61822 / % possible obs: 90.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Biso Wilson estimate: 16.7 Å2 / Limit h max: 62 / Limit h min: 4 / Limit k max: 44 / Limit k min: 4 / Limit l max: 60 / Limit l min: 0 / Observed criterion F max: 3938787.78 / Observed criterion F min: 21.7 / Rsym value: 0.159 / Net I/σ(I): 11.2
Reflection shellResolution: 2.41→2.49 Å / Mean I/σ(I) obs: 4.2 / Num. unique all: 6028 / Rsym value: 0.391 / % possible all: 89.1

-
Processing

Software
NameVersionClassificationNB
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MWV

1mwv
PDB Unreleased entry


Resolution: 2.41→23.71 Å / Rfactor Rfree error: 0.003 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.268 6260 10.1 %RANDOM
Rwork0.211 ---
all-68475 --
obs-61822 90.3 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 41.3955 Å2 / ksol: 0.36149 e/Å3
Displacement parametersBiso max: 89.42 Å2 / Biso mean: 38.34 Å2 / Biso min: 14.45 Å2
Baniso -1Baniso -2Baniso -3
1--19.35 Å20 Å20 Å2
2---19.35 Å20 Å2
3---38.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.6 Å0.54 Å
Luzzati d res high-2.41
Refinement stepCycle: LAST / Resolution: 2.41→23.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11058 0 122 703 11883
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_torsion_deg22.1
X-RAY DIFFRACTIONx_torsion_impr_deg1.3
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.41-2.520.3967159.60.3767120.0158449742787.9
2.52-2.650.357782100.31570610.0138457784392.7
2.65-2.820.32978810.10.27170480.0128476783692.4
2.82-3.040.31381110.40.24469940.0118495780591.9
3.04-3.340.28580410.30.20969940.018502779891.7
3.34-3.820.25983310.70.19369450.0098562777890.8
3.82-4.810.2127539.80.14869270.0088662768088.7
4.81-23.710.21377410.10.17268810.0088949765585.5

+
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