[English] 日本語
Yorodumi
- PDB-3wr3: Crystal structure of the anaerobic DesB-gallate complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3wr3
TitleCrystal structure of the anaerobic DesB-gallate complex
ComponentsGallate dioxygenase
KeywordsOXIDOREDUCTASE / type II extradiol dioxygenase / domain-swap dimer / extradiol dioxygenase / Fe2+ binding
Function / homology
Function and homology information


: / dioxygenase activity / ferrous iron binding
Similarity search - Function
Gallate dioxygenase, N-terminal / Gallate dioxygenase, C-terminal / Protocatechuate 4,5-dioxygenase; Chain A / Dioxygenase LigAB, LigA subunit / Protocatechuate 4,5-dioxygenase; Chain B / LigB-like / Extradiol ring-cleavage dioxygenase LigAB, LigA subunit / Dioxygenase LigAB, LigA subunit superfamily / Aromatic-ring-opening dioxygenase LigAB, LigA subunit / Extradiol ring-cleavage dioxygenase, class III enzyme, subunit B ...Gallate dioxygenase, N-terminal / Gallate dioxygenase, C-terminal / Protocatechuate 4,5-dioxygenase; Chain A / Dioxygenase LigAB, LigA subunit / Protocatechuate 4,5-dioxygenase; Chain B / LigB-like / Extradiol ring-cleavage dioxygenase LigAB, LigA subunit / Dioxygenase LigAB, LigA subunit superfamily / Aromatic-ring-opening dioxygenase LigAB, LigA subunit / Extradiol ring-cleavage dioxygenase, class III enzyme, subunit B / Catalytic LigB subunit of aromatic ring-opening dioxygenase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / 3,4,5-trihydroxybenzoic acid / Gallate dioxygenase
Similarity search - Component
Biological speciesSphingobium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSugimoto, K. / Senda, M. / Kasai, D. / Fukuda, M. / Masai, E. / Senda, T.
CitationJournal: Plos One / Year: 2014
Title: Molecular Mechanism of Strict Substrate Specificity of an Extradiol Dioxygenase, DesB, Derived from Sphingobium sp. SYK-6
Authors: Sugimoto, K. / Senda, M. / Kasai, D. / Fukuda, M. / Masai, E. / Senda, T.
History
DepositionFeb 13, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Advisory / Experimental preparation / Category: exptl_crystal_grow / pdbx_unobs_or_zero_occ_atoms
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.2Nov 8, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_conn / 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_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_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_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.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_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: Gallate dioxygenase
B: Gallate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,1885
Polymers93,9062
Non-polymers2823
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10040 Å2
ΔGint-76 kcal/mol
Surface area29030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.350, 64.020, 118.483
Angle α, β, γ (deg.)90.00, 97.14, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Gallate dioxygenase


Mass: 46953.164 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingobium (bacteria) / Strain: SYK-6 / Gene: desB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: G2IKE5, Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-GDE / 3,4,5-trihydroxybenzoic acid / Gallate


Mass: 170.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O5

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.75
Details: 25% PEG8000, 0.1M sodium acetate, 0.1M HEPES-NaOH, pH 7.75, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 12, 2010
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 75677 / Num. obs: 68790 / % possible obs: 90.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.3→2.42 Å / % possible all: 91.7

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
PHENIX(phenix.refine: dev_1539)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WKU

3wku


Resolution: 2.5→19.695 Å / SU ML: 0.41 / σ(F): 1.12 / Phase error: 38.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.313 1402 5 %Random
Rwork0.2313 ---
all0.2355 ---
obs0.2355 28045 91.08 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→19.695 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6449 0 14 0 6463
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016650
X-RAY DIFFRACTIONf_angle_d1.3359020
X-RAY DIFFRACTIONf_dihedral_angle_d15.9162408
X-RAY DIFFRACTIONf_chiral_restr0.052932
X-RAY DIFFRACTIONf_plane_restr0.0081188
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.54540.43261460.29642728X-RAY DIFFRACTION90
2.5454-2.59420.34431270.29642517X-RAY DIFFRACTION88
2.5942-2.64710.38731380.29982647X-RAY DIFFRACTION89
2.6471-2.70450.44511430.31532706X-RAY DIFFRACTION92
2.7045-2.76720.41251360.27942593X-RAY DIFFRACTION88
2.7672-2.83620.36671310.28942481X-RAY DIFFRACTION86
2.8362-2.91270.40271350.30632581X-RAY DIFFRACTION85
2.9127-2.99810.4111310.31772486X-RAY DIFFRACTION85
2.9981-3.09450.48831370.30712620X-RAY DIFFRACTION89
3.0945-3.20470.38831430.28982772X-RAY DIFFRACTION93
3.2047-3.33240.36021490.26762743X-RAY DIFFRACTION96
3.3324-3.48330.33741470.24552810X-RAY DIFFRACTION95
3.4833-3.66580.33241430.24332714X-RAY DIFFRACTION93
3.6658-3.89380.30851490.22982784X-RAY DIFFRACTION94
3.8938-4.19180.34121450.21922647X-RAY DIFFRACTION91
4.1918-4.60880.23661480.18512771X-RAY DIFFRACTION94
4.6088-5.26450.2381460.18212792X-RAY DIFFRACTION95
5.2645-6.59120.24491480.19912821X-RAY DIFFRACTION96
6.5912-19.69550.24131380.16942668X-RAY DIFFRACTION91

+
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://pdbjlvh1.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