[English] 日本語
Yorodumi
- PDB-3hgi: Crystal structure of Catechol 1,2-Dioxygenase from the gram-posit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3hgi
TitleCrystal structure of Catechol 1,2-Dioxygenase from the gram-positive Rhodococcus opacus 1CP
ComponentsCatechol 1,2-dioxygenase
KeywordsOXIDOREDUCTASE / beta sandwich / Aromatic hydrocarbons catabolism / Dioxygenase / Iron / Metal-binding
Function / homology
Function and homology information


catechol-containing compound metabolic process / catechol 1,2-dioxygenase / catechol 1,2-dioxygenase activity / catabolic process / ferric iron binding
Similarity search - Function
Catechol 1,2-dioxygenase multimerisation domain-like / Catechol 1,2-dioxygenase, actinobacteria / Catechol 1,2-dioxygenase multimerisation domain / Chlorocatechol 1,2-dioxygenase / Catechol dioxygenase, N-terminal / Catechol dioxygenase N terminus / Helicase, Ruva Protein; domain 3 / Protocatechuate 3,4-Dioxygenase, subunit A / Aromatic compound dioxygenase / Intradiol ring-cleavage dioxygenases signature. ...Catechol 1,2-dioxygenase multimerisation domain-like / Catechol 1,2-dioxygenase, actinobacteria / Catechol 1,2-dioxygenase multimerisation domain / Chlorocatechol 1,2-dioxygenase / Catechol dioxygenase, N-terminal / Catechol dioxygenase N terminus / Helicase, Ruva Protein; domain 3 / Protocatechuate 3,4-Dioxygenase, subunit A / Aromatic compound dioxygenase / Intradiol ring-cleavage dioxygenases signature. / : / Intradiol ring-cleavage dioxygenase, C-terminal / Intradiol ring-cleavage dioxygenase, core / Dioxygenase / Helix non-globular / Special / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-6PL / BENZOIC ACID / CARBONATE ION / : / Catechol 1,2-dioxygenase
Similarity search - Component
Biological speciesRhodococcus opacus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsFerraroni, M. / Matera, I. / Briganti, F. / Scozzafava, A.
CitationJournal: J.Struct.Biol. / Year: 2010
Title: Catechol 1,2-dioxygenase from the Gram-positive Rhodococcus opacus 1CP: Quantitative structure/activity relationship and the crystal structures of native enzyme and catechols adducts.
Authors: Matera, I. / Ferraroni, M. / Kolomytseva, M. / Golovleva, L. / Scozzafava, A. / Briganti, F.
History
DepositionMay 14, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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: Catechol 1,2-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7265
Polymers30,7251
Non-polymers1,0014
Water4,252236
1
A: Catechol 1,2-dioxygenase
hetero molecules

A: Catechol 1,2-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,45210
Polymers61,4502
Non-polymers2,0028
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area10310 Å2
ΔGint-74 kcal/mol
Surface area22820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.794, 38.118, 76.065
Angle α, β, γ (deg.)90.00, 94.21, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-320-

HOH

21A-457-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Catechol 1,2-dioxygenase / 1 / 2-CTD


Mass: 30725.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: grown on benzoate / Source: (natural) Rhodococcus opacus (bacteria) / Strain: 1CP / References: UniProt: P95607, catechol 1,2-dioxygenase

-
Non-polymers , 5 types, 240 molecules

#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3
#4: Chemical ChemComp-6PL / (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE / 1-PALMITOYL-2-STEAROYL-SN-GLYCERO-3-PHOSPHOCHOLINE


Mass: 763.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H85NO8P / Comment: phospholipid*YM
#5: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsTHE SEQUENCE MATCHES THE GENBANK DEPOSITION WITH ACCESSION CODE CAA67941, IN WHICH ALL 280 RESIDUES ...THE SEQUENCE MATCHES THE GENBANK DEPOSITION WITH ACCESSION CODE CAA67941, IN WHICH ALL 280 RESIDUES ARE PRESENT.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.78 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 39% PEG400, 0.1 M Hepes, 0.1 M magnesium chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.949 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 30, 2005
RadiationMonochromator: Fixed exit double crystal Si [111], horizontally focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.949 Å / Relative weight: 1
ReflectionResolution: 1.94→22.8 Å / Num. obs: 19038 / % possible obs: 98.5 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 11.1
Reflection shellResolution: 1.94→2.05 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.264 / Mean I/σ(I) obs: 2.6 / Num. unique all: 2662 / Rsym value: 0.264 / % possible all: 95.6

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.5.0044refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BOY

2boy


Resolution: 1.94→20 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.894 / SU B: 5.232 / SU ML: 0.15 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.202 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27755 965 5.1 %RANDOM
Rwork0.1986 ---
obs0.20259 18056 98.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.67 Å2
Baniso -1Baniso -2Baniso -3
1-1.41 Å20 Å22.33 Å2
2--1.14 Å20 Å2
3----2.21 Å2
Refinement stepCycle: LAST / Resolution: 1.94→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2018 0 55 236 2309
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222137
X-RAY DIFFRACTIONr_angle_refined_deg1.5731.9662904
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4255259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.14224.94999
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.40815323
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.992159
X-RAY DIFFRACTIONr_chiral_restr0.1130.2307
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211658
X-RAY DIFFRACTIONr_mcbond_it0.8741.51295
X-RAY DIFFRACTIONr_mcangle_it1.47422088
X-RAY DIFFRACTIONr_scbond_it2.3533842
X-RAY DIFFRACTIONr_scangle_it3.6174.5815
LS refinement shellResolution: 1.94→1.99 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 62 -
Rwork0.304 1245 -
obs--93.09 %

+
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