[English] 日本語
Yorodumi
- PDB-5znh: Catechol 2,3-dioxygenase with 4-methyl catechol from Diaphorobact... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5znh
TitleCatechol 2,3-dioxygenase with 4-methyl catechol from Diaphorobacter sp DS2
ComponentsCatechol 2,3-dioxygenase, extradiol protein
KeywordsOXIDOREDUCTASE / complex with 4-methylcatechol
Function / homology
Function and homology information


catechol 2,3-dioxygenase / catechol 2,3-dioxygenase activity / : / ferrous iron binding
Similarity search - Function
Catechol 2,3 dioxygenase / Extradiol ring-cleavage dioxygenase, class I /II / Extradiol ring-cleavage dioxygenases signature. / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase ...Catechol 2,3 dioxygenase / Extradiol ring-cleavage dioxygenase, class I /II / Extradiol ring-cleavage dioxygenases signature. / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Roll / Alpha Beta
Similarity search - Domain/homology
: / 4-METHYLCATECHOL / DI(HYDROXYETHYL)ETHER / Metapyrocatechase
Similarity search - Component
Biological speciesDiaphorobacter sp. DS2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMishra, K. / Arya, C.K. / Subramaniyan, R. / Ramanathan, G.
Funding support India, 5items
OrganizationGrant numberCountry
BT/IN/SWEDEN/41/SR/2013 India
BT/PR5081/INF/156/2012 India
BT/PR12422/MED/31/287/214 India
BT/INF/22/SP22660/2017 India
09/092(0869)/2013-EMR-I India
CitationJournal: To Be Published
Title: catechol 2,3-dioxygenase with 4-methyl catechol from Diaphorobacter sp DS2
Authors: Mishra, K. / Arya, C.K. / Subramaniyan, R. / Ramanathan, G.
History
DepositionApr 9, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Catechol 2,3-dioxygenase, extradiol protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3086
Polymers34,9191
Non-polymers3885
Water59433
1
A: Catechol 2,3-dioxygenase, extradiol protein
hetero molecules

A: Catechol 2,3-dioxygenase, extradiol protein
hetero molecules

A: Catechol 2,3-dioxygenase, extradiol protein
hetero molecules

A: Catechol 2,3-dioxygenase, extradiol protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,23124
Polymers139,6784
Non-polymers1,55320
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
crystal symmetry operation8_556x-y,-y,-z+11
crystal symmetry operation11_656-x+y+1,y,-z+11
Buried area15550 Å2
ΔGint-167 kcal/mol
Surface area41380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.894, 101.894, 114.369
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Catechol 2,3-dioxygenase, extradiol protein /


Mass: 34919.488 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Diaphorobacter sp. DS2 (bacteria)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A4V8GZK8*PLUS, catechol 2,3-dioxygenase

-
Non-polymers , 6 types, 38 molecules

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


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-MCT / 4-METHYLCATECHOL / 4-METHYL-1,2-BENZENEDIOL / 4-Methylcatechol


Mass: 124.137 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.45 Å3/Da / Density % sol: 49.88 % / Description: Diamond shaped crystal
Crystal growTemperature: 291.4 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% v/v PEG, 0.1M HEPES sodium salt pH 7.5, 0.2M Magnesium chloride

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.0053 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 10, 2018
RadiationMonochromator: liquid nitrogen cooled dual crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0053 Å / Relative weight: 1
ReflectionResolution: 2.4→47.99 Å / Num. obs: 14302 / % possible obs: 100 % / Redundancy: 10.2 % / Biso Wilson estimate: 45.77 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.023 / Rrim(I) all: 0.074 / Net I/σ(I): 22.4 / Num. measured all: 145849 / Scaling rejects: 155
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.4-2.4910.60.6741548614670.8970.2150.7093.7100
8.98-47.9980.03727433430.9990.0120.03952.699.5

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Aimless0.6.2data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HQ0

3hq0


Resolution: 2.4→47.989 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2393 716 5.02 %
Rwork0.1988 13539 -
obs0.2009 14255 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.48 Å2 / Biso mean: 53.5438 Å2 / Biso min: 27.03 Å2
Refinement stepCycle: final / Resolution: 2.4→47.989 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2454 0 22 33 2509
Biso mean--55.96 47.38 -
Num. residues----314
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.4001-2.58540.33251340.242526372771
2.5854-2.84560.26381330.231826712804
2.8456-3.25730.28771490.223226572806
3.2573-4.10350.21261470.192726922839
4.1035-47.99860.22051530.179228823035
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)
12.38810.23290.21751.9877-0.20631.53770.30190.70890.2743-0.3698-0.19090.0788-0.20730.101-0.110.35230.25170.09050.79030.11690.421732.837112.435937.2124
22.8432-0.02030.63831.618-0.5251.16870.3590.44760.2109-0.2031-0.17910.4659-0.3048-0.4515-0.14340.31140.25550.00120.75040.02960.507314.491411.878943.9086
31.93030.23220.28062.23930.2261.03860.35520.3590.2202-0.198-0.27240.1712-0.1427-0.1251-0.12610.29470.19460.0580.6383-0.01060.351728.704210.459646.4032
41.71010.06760.00251.1893-0.50921.52190.3064-0.10450.24490.101-0.24590.1491-0.2039-0.0127-0.09590.30820.03780.11660.5315-0.06080.463531.003814.815756.7653
52.13810.12120.42031.6256-0.60531.71220.3897-0.27980.64770.0655-0.6125-0.0831-0.18390.6179-0.09460.35780.06990.17280.68280.04850.583642.683216.101451.5949
61.9135-0.48630.64411.6396-0.56691.6290.5557-0.26560.58420.1597-0.6239-0.5266-0.51430.4179-0.04290.4111-0.11170.16170.642-0.07050.553536.329516.96263.4269
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 62 )A1 - 62
2X-RAY DIFFRACTION2chain 'A' and (resid 63 through 103 )A63 - 103
3X-RAY DIFFRACTION3chain 'A' and (resid 104 through 164 )A104 - 164
4X-RAY DIFFRACTION4chain 'A' and (resid 165 through 240 )A165 - 240
5X-RAY DIFFRACTION5chain 'A' and (resid 241 through 274 )A241 - 274
6X-RAY DIFFRACTION6chain 'A' and (resid 275 through 314 )A275 - 314

+
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