[English] 日本語
Yorodumi
- PDB-3njz: Crystal Structure of Salicylate 1,2-dioxygenase from Pseudoaminob... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3njz
TitleCrystal Structure of Salicylate 1,2-dioxygenase from Pseudoaminobacter salicylatoxidans Adducts with salicylate
ComponentsGentisate 1,2-dioxygenase
KeywordsOXIDOREDUCTASE / BETA-SANDWICH
Function / homology
Function and homology information


dioxygenase activity / metal ion binding
Similarity search - Function
: / Cupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / 2-HYDROXYBENZOIC ACID / Gentisate 1,2-dioxygenase
Similarity search - Component
Biological speciesPseudaminobacter salicylatoxidans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsFerraroni, M. / Briganti, F. / Matera, I.
CitationJournal: J.Struct.Biol. / Year: 2012
Title: Crystal structures of salicylate 1,2-dioxygenase-substrates adducts: A step towards the comprehension of the structural basis for substrate selection in class III ring cleaving dioxygenases.
Authors: Ferraroni, M. / Matera, I. / Steimer, L. / Burger, S. / Scozzafava, A. / Stolz, A. / Briganti, F.
History
DepositionJun 18, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2012Group: Database references
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _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.ptnr1_label_seq_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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: Gentisate 1,2-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5235
Polymers41,1441
Non-polymers3784
Water5,837324
1
A: Gentisate 1,2-dioxygenase
hetero molecules

A: Gentisate 1,2-dioxygenase
hetero molecules

A: Gentisate 1,2-dioxygenase
hetero molecules

A: Gentisate 1,2-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,09020
Polymers164,5784
Non-polymers1,51316
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area28110 Å2
ΔGint-240 kcal/mol
Surface area48780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.652, 86.961, 166.465
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

-
Components

#1: Protein Gentisate 1,2-dioxygenase /


Mass: 41144.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudaminobacter salicylatoxidans (bacteria)
Strain: BN12 / Plasmid: pET28A / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q67FT0, gentisate 1,2-dioxygenase
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-SAL / 2-HYDROXYBENZOIC ACID / SALICYLIC ACID / Salicylic acid


Mass: 138.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 324 / 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: 3.37 Å3/Da / Density % sol: 63.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 8
Details: 8% PEG10000, pH 8.0, vapor diffusion, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 4, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→83.333 Å / Num. all: 32880 / Num. obs: 32880 / % possible obs: 99.9 % / Redundancy: 4.3 % / Biso Wilson estimate: 25.632 Å2 / Rmerge(I) obs: 0.122 / Rsym value: 0.122 / Net I/σ(I): 11.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.1-2.214.30.4231.72029247580.42399.9
2.21-2.3540.4610.51782444910.46199.9
2.35-2.514.40.2253.21850642210.225100
2.51-2.714.30.2191.61703239320.21999.9
2.71-2.974.40.125.71625536700.12100
2.97-3.324.40.0847.71461032920.084100
3.32-3.834.20.1113.31220629250.111100
3.83-4.74.30.0714.91062424920.071100
4.7-6.644.30.0414.1855819760.04100
6.64-47.2984.10.03615.7459211230.03698.9

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.19data scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.889 / WRfactor Rfree: 0.2106 / WRfactor Rwork: 0.1746 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8187 / SU B: 4.038 / SU ML: 0.106 / SU R Cruickshank DPI: 0.1742 / SU Rfree: 0.1604 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2309 1644 5.1 %RANDOM
Rwork0.1913 ---
obs0.1933 32423 98.54 %-
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 max: 62.99 Å2 / Biso mean: 25.8136 Å2 / Biso min: 10.55 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20 Å20 Å2
2--1.22 Å20 Å2
3----1.7 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2845 0 23 324 3192
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222978
X-RAY DIFFRACTIONr_angle_refined_deg1.481.9514053
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6685371
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.41523.165139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.19415467
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8411525
X-RAY DIFFRACTIONr_chiral_restr0.0980.2427
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212329
X-RAY DIFFRACTIONr_mcbond_it0.6731.51822
X-RAY DIFFRACTIONr_mcangle_it1.25622940
X-RAY DIFFRACTIONr_scbond_it2.19631156
X-RAY DIFFRACTIONr_scangle_it3.4624.51109
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 129 -
Rwork0.226 2288 -
all-2417 -
obs--99.83 %

+
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