[English] 日本語
Yorodumi
- PDB-2boy: Crystal structure of 3-ChloroCatechol 1,2-Dioxygenase from Rhodoc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2boy
TitleCrystal structure of 3-ChloroCatechol 1,2-Dioxygenase from Rhodococcus Opacus 1CP
Components3-CHLOROCATECHOL 1,2-DIOXYGENASE
KeywordsOXIDOREDUCTASE / BETA BARREL / DIOXYGENASE
Function / homology
Function and homology information


catechol-containing compound metabolic process / catechol 1,2-dioxygenase / catechol 1,2-dioxygenase activity / ferric iron binding
Similarity search - Function
Chlorocatechol 1,2-dioxygenase / Catechol dioxygenase, N-terminal / Catechol dioxygenase N terminus / 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 ...Chlorocatechol 1,2-dioxygenase / Catechol dioxygenase, N-terminal / Catechol dioxygenase N terminus / 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 / Sandwich / Mainly Beta
Similarity search - Domain/homology
BENZHYDROXAMIC ACID / : / Chem-LPP / Chlorocatechol 1,2-dioxygenase
Similarity search - Component
Biological speciesRHODOCOCCUS OPACUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsFerraroni, M. / Solyanikova, I.P. / Kolomytseva, M.P. / Scozzafava, A. / Golovleva, L.A. / Briganti, F.
Citation
Journal: J. Mol. Biol. / Year: 2006
Title: Crystal structure of 3-chlorocatechol 1,2-dioxygenase key enzyme of a new modified ortho-pathway from the Gram-positive Rhodococcus opacus 1CP grown on 2-chlorophenol.
Authors: Ferraroni, M. / Kolomytseva, M.P. / Solyanikova, I.P. / Scozzafava, A. / Golovleva, L.A. / Briganti, F.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Preliminary Crystallographic Analysis of 3-Chlorocatechol 1,2 Dioxygenase of a New Modified Ortho-Patway from the Gram Positive Rhodococcus Opacus 1Cp Grown on 2-Chlorophenol
Authors: Ferraroni, M. / Ruiz Tarifa, M.Y. / Scozzafava, A. / Solyanikova, I.P. / Kolomytseva, M.P. / Golovleva, L.A. / Briganti, F.
History
DepositionApr 15, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 6, 2018Group: Data collection / Database references / Derived calculations
Category: citation / pdbx_struct_assembly ...citation / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details
Revision 1.4Dec 19, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_struct_conn_angle / pdbx_validate_close_contact ...pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_conn_type
Revision 1.5May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.6May 29, 2019Group: Data collection / Other / Category: pdbx_database_proc / pdbx_database_status
Item: _pdbx_database_status.date_of_sf_release / _pdbx_database_status.status_code_sf
Revision 1.7Dec 13, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 3-CHLOROCATECHOL 1,2-DIOXYGENASE
B: 3-CHLOROCATECHOL 1,2-DIOXYGENASE
C: 3-CHLOROCATECHOL 1,2-DIOXYGENASE
D: 3-CHLOROCATECHOL 1,2-DIOXYGENASE
E: 3-CHLOROCATECHOL 1,2-DIOXYGENASE
F: 3-CHLOROCATECHOL 1,2-DIOXYGENASE
G: 3-CHLOROCATECHOL 1,2-DIOXYGENASE
H: 3-CHLOROCATECHOL 1,2-DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,17648
Polymers225,0528
Non-polymers7,12440
Water32,4271800
1
A: 3-CHLOROCATECHOL 1,2-DIOXYGENASE
hetero molecules

E: 3-CHLOROCATECHOL 1,2-DIOXYGENASE
hetero molecules


  • defined by author
  • 58 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)58,02011
Polymers56,2632
Non-polymers1,7579
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_445x-1,y-1,z1
2
F: 3-CHLOROCATECHOL 1,2-DIOXYGENASE
hetero molecules

B: 3-CHLOROCATECHOL 1,2-DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,04412
Polymers56,2632
Non-polymers1,78110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
3
G: 3-CHLOROCATECHOL 1,2-DIOXYGENASE
hetero molecules

C: 3-CHLOROCATECHOL 1,2-DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,06813
Polymers56,2632
Non-polymers1,80511
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
4
D: 3-CHLOROCATECHOL 1,2-DIOXYGENASE
H: 3-CHLOROCATECHOL 1,2-DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,04412
Polymers56,2632
Non-polymers1,78110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.179, 86.610, 93.447
Angle α, β, γ (deg.)85.37, 66.53, 76.94
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12E
22F
32G
42H

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A1 - 254
2116B1 - 254
3116C1 - 254
4116D1 - 254
1126E1 - 254
2126F1 - 254
3126G1 - 254
4126H1 - 254

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(0.92294, 0.34796, -0.16464), (0.15447, 0.05698, 0.98635), (0.35259, -0.93578, -0.00116)72.84505, 37.35315, 0.1059
2given(0.92294, 0.34796, -0.16464), (0.15447, 0.05698, 0.98635), (0.35259, -0.93578, -0.00116)72.84505, 37.35315, 0.1059
3given(0.92789, 0.20751, 0.30978), (0.29883, 0.08298, -0.95069), (-0.22298, 0.97471, 0.01498)39.67403, -0.30892, 47.34713
4given(0.83451, 0.53174, 0.14439), (0.5315, -0.84594, 0.0435), (0.14528, 0.04044, -0.98856)29.66515, 37.00785, 47.1558
5given(0.92195, 0.37481, -0.09758), (0.09938, 0.01458, 0.99494), (0.37434, -0.92699, -0.02381)-74.61449, -58.53592, 40.48733
6given(0.9253, 0.22898, 0.30232), (0.28326, 0.11277, -0.95239), (-0.25217, 0.96688, 0.03948)-54.82457, 45.53782, -8.82951
7given(0.83355, 0.53696, 0.12988), (0.53803, -0.8424, 0.0297), (0.12536, 0.04512, -0.99108)-100.74558, 53.21134, 30.71702

-
Components

-
Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
3-CHLOROCATECHOL 1,2-DIOXYGENASE


Mass: 28131.559 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) RHODOCOCCUS OPACUS (bacteria) / Strain: 1CP / References: UniProt: Q8G9L3, catechol 1,2-dioxygenase

-
Non-polymers , 5 types, 1840 molecules

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


Mass: 55.845 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-BHO / BENZHYDROXAMIC ACID


Mass: 137.136 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C7H7NO2
#4: Chemical
ChemComp-LPP / 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE / 1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE / L-B,G-DIPALMITOYL-A-PHOSPHATIDIC ACID DISODIUM SALT / 3-SN-PHOSPHATIDIC ACID / 1,2-DIPALMITOYLDISODIUM SALT


Mass: 648.891 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C35H69O8P / Comment: phospholipid*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1800 / 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: 2.59 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 296 K / pH: 7.5
Details: 15% PEG 8000, 0.3 M MAGNESIUM ACETATE, 100 MM HEPES PH 7.5, 5% GLYCEROL 296 K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 16, 2002 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→84.5 Å / Num. obs: 1777980 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 23.5
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 1.57 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 2.8 / % possible all: 82.6

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1S9A

1s9a


Resolution: 1.9→84.51 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.206 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.219 8943 5 %RANDOM
Rwork0.176 ---
obs0.178 169019 97.2 %-
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: 27.54 Å2
Baniso -1Baniso -2Baniso -3
1-0.89 Å20.43 Å20.47 Å2
2---0.56 Å20.39 Å2
3----0.96 Å2
Refinement stepCycle: LAST / Resolution: 1.9→84.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15553 0 378 1800 17731
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02116559
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5711.9522464
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.42752006
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.130.22365
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212791
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2140.28074
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.21543
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.2353
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1890.2129
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9541.510014
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.7216119
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.536545
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9234.56345
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

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1932loose positional0.435
12B1932loose positional0.395
13C1932loose positional0.385
14D1932loose positional0.275
21E1896loose positional0.35
22F1896loose positional0.365
23G1896loose positional0.295
24H1896loose positional0.35
11A1932loose thermal2.3610
12B1932loose thermal2.0210
13C1932loose thermal1.9510
14D1932loose thermal2.2410
21E1896loose thermal2.510
22F1896loose thermal2.9210
23G1896loose thermal3.3410
24H1896loose thermal1.7310
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.289 614
Rwork0.237 11717

+
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