[English] 日本語
Yorodumi
- PDB-2ccd: Crystal structure of the catalase-peroxidase (KatG) and S315T mut... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ccd
TitleCrystal structure of the catalase-peroxidase (KatG) and S315T mutant from Mycobacterium tuberculosis
ComponentsPEROXIDASE/CATALASE T
KeywordsOXIDOREDUCTASE / KATG / HYDROGEN PEROXIDE / IRON / METAL-BINDING
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 / cell wall / NADH binding / catalase-peroxidase / catalase activity / NADPH binding / peptidoglycan-based cell wall / positive regulation of DNA repair / hydrogen peroxide catabolic process ...oxidoreductase activity, acting on a heme group of donors, nitrogenous group as acceptor / Tolerance of reactive oxygen produced by macrophages / cell wall / NADH binding / catalase-peroxidase / catalase activity / NADPH binding / peptidoglycan-based cell wall / positive regulation of DNA repair / 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: 2.1 Å
AuthorsYu, H. / Sacchettini, J.C.
CitationJournal: Biochemistry / Year: 2006
Title: Hydrogen Peroxide-Mediated Isoniazid Activation Catalyzed by Mycobacterium Tuberculosis Catalase- Peroxidase (Katg) and its S315T Mutant.
Authors: Zhao, X. / Yu, H. / Yu, S. / Wang, F. / Sacchettini, J.C. / Magliozzo, R.S.
History
DepositionJan 16, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 19, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 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_conn
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_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
Revision 1.3Sep 2, 2026Group: Derived calculations / Structure summary
Category: pdbx_contact_author / pdbx_entry_details ...pdbx_contact_author / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_atom_coordination / pdbx_nonpoly_atom_coordination_sphere / pdbx_nonpoly_atom_coordination_sphere_order / struct_site
Item: _pdbx_contact_author.country / _pdbx_contact_author.organization_type ..._pdbx_contact_author.country / _pdbx_contact_author.organization_type / _pdbx_entry_details.has_protein_modification / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Description: Metalloprotein remediation / Provider: repository / Type: Remediation

-
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)162,6364
Polymers161,4032
Non-polymers1,2332
Water10,719595
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11320 Å2
ΔGint-103.6 kcal/mol
Surface area49470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.807, 149.807, 154.493
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A26 - 741
2111B26 - 741

-
Components

#1: Protein PEROXIDASE/CATALASE T / KATG S315T / CATALASE-PEROXIDASE T


Mass: 80701.633 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: HEME PROTORPHYRIN IX FE(III) / Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: MTB H37RV / Plasmid: PSY31 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): UM262 / References: UniProt: Q08129, UniProt: P9WIE5*PLUS
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 595 / Source method: isolated from a natural source / Formula: H2O
Compound detailsHAS A DOUBLE FUNCTION: EXHIBITS BOTH A CATALASE AND BROAD- SPECTRUM PEROXIDASE ACTIVITIES. POSSIBLE ...HAS A DOUBLE FUNCTION: EXHIBITS BOTH A CATALASE AND BROAD- SPECTRUM PEROXIDASE ACTIVITIES. POSSIBLE ROLE IN THE INTRACELLULAR SURVIVAL OF MYCOBACTERIA ENGINEERED RESIDUE IN CHAIN A, SER 315 TO THR ENGINEERED RESIDUE IN CHAIN B, SER 315 TO THR
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.2 %
Crystal growpH: 4.6
Details: 6% PEG4000, 0.1M NA ACETATE, PH4.6, 0.17MM N-DODECYL-B-D-MALTOSIDE PROTEIN CONCENTRATION OF 16MG/ML, pH 4.60

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.974
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 21, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.974 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 76312 / % possible obs: 78.5 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 10
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 1.9 / % possible all: 64

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
XTALVIEWphasing
REFMAC5.2.0005refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CC4

2cc4
PDB Unreleased entry


Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.862 / SU B: 17.759 / SU ML: 0.215 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.337 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.276 3986 5 %RANDOM
Rwork0.23 ---
obs0.232 76312 78.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.27 Å2
Baniso -1Baniso -2Baniso -3
1--1.5 Å20 Å20 Å2
2---1.5 Å20 Å2
3---2.99 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11034 0 86 595 11715
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02211435
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3921.97215590
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9651422
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.85424.023512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.057151754
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2741572
X-RAY DIFFRACTIONr_chiral_restr0.0920.21626
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028924
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2150.26193
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.27844
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2818
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.253
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2350.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5491.57211
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.796211326
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.33834898
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.9424.54260
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 5517 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.380.05
tight thermal1.470.5
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.328 231
Rwork0.321 4471
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.55460.02510.24270.03950.12330.43540.05410.0188-0.15370.0742-0.0599-0.00640.0041-0.01490.00580.0096-0.0453-0.01020.0120.0274-0.025357.94518.61139.868
20.5587-0.0290.0710.20630.04510.13830.0391-0.03920.02150.0131-0.0187-0.06820.0106-0.0225-0.02040.0112-0.0117-0.02550.0046-0.0043-0.036679.7339.03647.808
30.4390.14140.15111.1168-0.00760.1644-0.03880.046-0.027-0.0650.0215-0.0427-0.0118-0.01890.01740.0268-0.00380.00680.04620.0109-0.140157.17533.50615.047
40.57960.31220.00280.68950.00380.06310.0413-0.0287-0.11990.0006-0.0531-0.0928-0.0201-0.02270.0119-0.0049-0.0051-0.0033-0.00910.0164-0.029840.078-5.5532.776
51.46640.62720.13580.72360.21560.19080.1222-0.2609-0.01070.127-0.17620.02750.0072-0.09290.0540.051-0.07070.01690.1084-0.0148-0.156538.71922.57761.367
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A26 - 60
2X-RAY DIFFRACTION1B26 - 60
3X-RAY DIFFRACTION2A61 - 433
4X-RAY DIFFRACTION2A1741
5X-RAY DIFFRACTION3A434 - 740
6X-RAY DIFFRACTION4B61 - 433
7X-RAY DIFFRACTION4B1741
8X-RAY DIFFRACTION5B434 - 740

+
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