[English] 日本語
Yorodumi
- PDB-3r1j: Crystal structure of Alpha-ketoglutarate-dependent taurine dioxyg... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3r1j
TitleCrystal structure of Alpha-ketoglutarate-dependent taurine dioxygenase from Mycobacterium avium, native form
ComponentsAlpha-ketoglutarate-dependent taurine dioxygenase
KeywordsOXIDOREDUCTASE / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


taurine dioxygenase / alkyl sulfatase / taurine dioxygenase activity / metal ion binding / cytoplasm
Similarity search - Function
: / Clavaminate synthase-like / Double-stranded beta-helix / TauD/TfdA-like domain / Taurine catabolism dioxygenase TauD, TfdA family / Taurine dioxygenase TauD-like superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Alpha-ketoglutarate-dependent sulfate ester dioxygenase / Alpha-ketoglutarate-dependent taurine dioxygenase
Similarity search - Component
Biological speciesMycobacterium avium (bacteria)
MethodX-RAY DIFFRACTION / molecular replacement / Resolution: 2.05 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Tuberculosis (Edinb) / Year: 2015
Title: Increasing the structural coverage of tuberculosis drug targets.
Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / ...Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / Gardberg, A.S. / Choi, R. / Hewitt, S.N. / Napuli, A.J. / Myers, J. / Barrett, L.K. / Zhang, Y. / Ferrell, M. / Mundt, E. / Thompkins, K. / Tran, N. / Lyons-Abbott, S. / Abramov, A. / Sekar, A. / Serbzhinskiy, D. / Lorimer, D. / Buchko, G.W. / Stacy, R. / Stewart, L.J. / Edwards, T.E. / Van Voorhis, W.C. / Myler, P.J.
History
DepositionMar 10, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 22, 2015Group: Database references
Revision 1.3Sep 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 / pdbx_struct_special_symmetry / 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_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_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: Alpha-ketoglutarate-dependent taurine dioxygenase
B: Alpha-ketoglutarate-dependent taurine dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,77010
Polymers67,3662
Non-polymers4048
Water5,873326
1
A: Alpha-ketoglutarate-dependent taurine dioxygenase
B: Alpha-ketoglutarate-dependent taurine dioxygenase
hetero molecules

A: Alpha-ketoglutarate-dependent taurine dioxygenase
B: Alpha-ketoglutarate-dependent taurine dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,54020
Polymers134,7324
Non-polymers80916
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area9880 Å2
ΔGint-117 kcal/mol
Surface area36770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.950, 105.310, 89.250
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-300-

CL

21B-301-

CL

31A-441-

HOH

41B-302-

HOH

-
Components

#1: Protein Alpha-ketoglutarate-dependent taurine dioxygenase


Mass: 33682.996 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium avium (bacteria) / Strain: 104 / Gene: MAV_4353 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A0QKQ0, UniProt: A0A0H2ZSG9*PLUS, taurine dioxygenase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / 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: 2.49 Å3/Da / Density % sol: 50.73 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Internal tracking number 218640E10. PACT screen condition E10: 0.2 M Na/K Phosphate, 20% PEG3350, MyavA.01188.b.A1 PW28977 at 28.9mg/ml. Cryoprotection: 25% ethylene glycol, VAPOR DIFFUSION, ...Details: Internal tracking number 218640E10. PACT screen condition E10: 0.2 M Na/K Phosphate, 20% PEG3350, MyavA.01188.b.A1 PW28977 at 28.9mg/ml. Cryoprotection: 25% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 290K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Feb 22, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.05→41.09 Å / Num. all: 42701 / Num. obs: 42570 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 28.296 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 15.84
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
2.05-2.13.40.4243.1104963124310399.3
2.1-2.160.3423.8114123026100
2.16-2.220.3514.512947296299.3
2.22-2.290.3095.712641281398.5
2.29-2.370.2596.113254275899.8
2.37-2.450.2396.813561270899.9
2.45-2.540.1918.313662261699.9
2.54-2.650.1789.313800249199.9
2.65-2.760.15910.714429240899.9
2.76-2.90.1313.515806229099.8
2.9-3.060.10316.616091222499.9
3.06-3.240.08519.6150342077100
3.24-3.470.06825.714171196899.9
3.47-3.740.05930.213225185499.9
3.74-4.10.04936.111965168999.6
4.1-4.580.03744.2110271542100
4.58-5.290.03544.29808137799.9
5.29-6.480.04368381118299.9
6.48-9.170.03242.86470936100
9.170.02454.8343054698

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å41.09 Å
Translation2.5 Å41.09 Å

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
StructureStudiodata collection
XDSdata reduction
RefinementMethod to determine structure: molecular replacement
Starting model: PDB ENTRY 1OIJ

1oij


Resolution: 2.05→37.78 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.942 / SU B: 7.217 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2 2139 5 %RANDOM
Rwork0.171 ---
all0.173 42570 --
obs0.173 42393 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.258 Å2
Baniso -1Baniso -2Baniso -3
1-1.04 Å20 Å20 Å2
2---0.15 Å20 Å2
3----0.89 Å2
Refinement stepCycle: LAST / Resolution: 2.05→37.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3832 0 17 326 4175
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0213993
X-RAY DIFFRACTIONr_bond_other_d0.0010.022711
X-RAY DIFFRACTIONr_angle_refined_deg1.3651.9375444
X-RAY DIFFRACTIONr_angle_other_deg0.86936523
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2965497
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.76921.897195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.55415625
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7961549
X-RAY DIFFRACTIONr_chiral_restr0.0850.2614
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214474
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02875
X-RAY DIFFRACTIONr_mcbond_it0.7021.52444
X-RAY DIFFRACTIONr_mcbond_other0.1951.5989
X-RAY DIFFRACTIONr_mcangle_it1.25223945
X-RAY DIFFRACTIONr_scbond_it2.0731549
X-RAY DIFFRACTIONr_scangle_it3.2694.51491
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 131 -
Rwork0.223 2957 -
all-3088 -
obs--98.88 %
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)
10.6027-0.54280.16011.1447-0.18541.0142-0.1532-0.1042-0.02160.17750.1896-0.04210.11970.0216-0.03640.16250.0662-0.00930.04370.00030.046641.52437.91859.798
21.1362-0.75190.00951.0739-0.12151.5867-0.221-0.3094-0.11990.18440.25870.151-0.0753-0.2152-0.03770.1210.12040.04340.14730.05270.06456.886.84972.301
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 296
2X-RAY DIFFRACTION2B5 - 292

+
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