[English] 日本語
Yorodumi
- PDB-5hsx: Crystal Structure of a Putative Alpha-ketoglutarate-dependent Tau... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5hsx
TitleCrystal Structure of a Putative Alpha-ketoglutarate-dependent Taurine Dioxygenase from Burkholderia xenovorans
ComponentsPutative alpha-ketoglutarate-dependent taurine dioxygenase
KeywordsOXIDOREDUCTASE / SSGCID / dioxygenase / Burkholderia xenovorans / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homologyClavaminate synthase-like / Double-stranded beta-helix / TauD/TfdA-like domain / Taurine catabolism dioxygenase TauD, TfdA family / Taurine dioxygenase TauD-like superfamily / dioxygenase activity / 4-Layer Sandwich / Alpha Beta / Putative alpha-ketoglutarate-dependent taurine dioxygenase
Function and homology information
Biological speciesBurkholderia xenovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of a Putative Alpha-ketoglutarate-dependent Taurine Dioxygenase from Burkholderia xenovorans
Authors: SSGCID / Dranow, D.M. / Mayclin, S.J. / Lorimer, D. / Edwards, T.E.
History
DepositionJan 26, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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_prerelease_seq / pdbx_struct_conn_angle / pdbx_struct_oper_list / 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_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative alpha-ketoglutarate-dependent taurine dioxygenase
B: Putative alpha-ketoglutarate-dependent taurine dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,95422
Polymers71,7312
Non-polymers1,22320
Water11,205622
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Putative alpha-ketoglutarate-dependent taurine dioxygenase
hetero molecules

A: Putative alpha-ketoglutarate-dependent taurine dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,95422
Polymers71,7312
Non-polymers1,22320
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area5150 Å2
ΔGint20 kcal/mol
Surface area25040 Å2
MethodPISA
3
B: Putative alpha-ketoglutarate-dependent taurine dioxygenase
hetero molecules

B: Putative alpha-ketoglutarate-dependent taurine dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,95422
Polymers71,7312
Non-polymers1,22320
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area3360 Å2
ΔGint-14 kcal/mol
Surface area23230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.190, 132.600, 55.570
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-790-

HOH

21A-805-

HOH

31B-787-

HOH

-
Components

#1: Protein Putative alpha-ketoglutarate-dependent taurine dioxygenase


Mass: 35865.480 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia xenovorans (strain LB400) (bacteria)
Strain: LB400 / Gene: Bxe_A2155 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q13YM5
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 622 / 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: 2.8 Å3/Da / Density % sol: 56.14 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7
Details: BuxeA.00024.i.B1.PS02500 at 24.3 mg/ml, protein was mixed 1:1 with JCSG+(b8): 10% (w/v) PEG-8000, 100 mM Tris base/HCl, pH = 7.0, 200 mM MgCl2, cryoprotected with 20% ethylene glycol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 10, 2015 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 75552 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 21.63 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rrim(I) all: 0.062 / Χ2: 1.007 / Net I/σ(I): 21.52 / Num. measured all: 554951
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.857.40.4873.7940900551955170.9440.523100
1.85-1.90.3774.8939849536853650.9610.40699.9
1.9-1.950.3046.0538782522952290.9750.327100
1.95-2.010.2357.937890509750950.9810.253100
2.01-2.080.17610.3336714494449440.990.189100
2.08-2.150.14712.3335586478247820.9930.158100
2.15-2.230.12214.6934456463146300.9950.131100
2.23-2.320.10316.9633224446544640.9960.11100
2.32-2.430.08819.6931663424942490.9970.094100
2.43-2.550.0821.8430513409740970.9970.087100
2.55-2.680.06525.6628886388838880.9980.07100
2.68-2.850.05630.2327428370237020.9980.061100
2.85-3.040.04934.6725522348634860.9990.053100
3.04-3.290.04239.7323637326632660.9990.046100
3.29-3.60.03843.7521525300530050.9990.041100
3.6-4.020.03547.1319368272927290.9990.037100
4.02-4.650.03150.417198244824470.9990.033100
4.65-5.690.02950.514538206720670.9990.031100
5.69-8.050.02849.8411376164716470.9990.03100
8.050.02451.0558969719430.9990.02697.1

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GY9

1gy9


Resolution: 1.8→35.098 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1808 2003 2.65 %
Rwork0.1551 73531 -
obs0.1558 75534 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.67 Å2 / Biso mean: 30.9751 Å2 / Biso min: 10.9 Å2
Refinement stepCycle: final / Resolution: 1.8→35.098 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4280 0 82 627 4989
Biso mean--46.56 38.83 -
Num. residues----549
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064521
X-RAY DIFFRACTIONf_angle_d0.8496169
X-RAY DIFFRACTIONf_chiral_restr0.055694
X-RAY DIFFRACTIONf_plane_restr0.006792
X-RAY DIFFRACTIONf_dihedral_angle_d14.8932624
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.7999-1.84490.25031230.218351755298
1.8449-1.89480.21931230.190751935316
1.8948-1.95050.21091520.173651925344
1.9505-2.01350.19631430.165951695312
2.0135-2.08540.19231260.158252335359
2.0854-2.16890.20251590.15451885347
2.1689-2.26760.18321560.149451885344
2.2676-2.38710.18831460.153652205366
2.3871-2.53670.19891610.157652365397
2.5367-2.73250.19431310.159152605391
2.7325-3.00730.16831490.155452555404
3.0073-3.44210.17561270.153753125439
3.4421-4.33550.18241480.139753695517
4.3355-35.10510.14771590.151655415700
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)
12.56310.7434-0.02220.38490.25851.1230.034-0.2627-0.35880.2102-0.17240.21750.5178-0.1998-0.0090.3216-0.17530.07020.2126-0.03030.311731.3744-30.4817-5.8845
22.52551.6044-0.28571.1425-0.43080.3862-0.04120.17330.2562-0.07240.02020.47520.1328-0.14040.04690.2115-0.0601-0.01590.2731-0.06280.332528.1853-14.4977-18.9366
31.090.51440.34450.70680.24320.59360.0785-0.0954-0.05770.1017-0.17770.11160.2238-0.14530.07360.1328-0.06340.01630.1992-0.03310.161540.1054-15.9408-9.0798
40.75930.5204-0.07121.42020.3690.49840.0471-0.0838-0.0158-0.0131-0.17140.18730.1038-0.12350.09090.1124-0.0471-0.00040.2152-0.03120.149640.8455-10.3552-8.2405
52.57271.05821.88523.87692.59432.3393-0.02360.35970.0056-0.4816-0.00950.087-0.4218-0.0370.01380.2207-0.0505-0.00950.247-0.04180.265529.6022-21.1702-22.6535
61.36461.49-0.8154.038-0.26181.470.1174-0.43470.32440.1869-0.25890.6508-0.0222-0.3093-0.01040.1764-0.09810.06530.3689-0.12360.280732.6217-5.7952.8301
73.39970.53290.62157.39133.92214.6416-0.03930.4141-0.4824-0.0688-0.23690.44110.454-0.54030.17210.28-0.03170.00720.2075-0.08760.288343.1235-33.687-32.4049
81.5519-1.0919-0.74241.95370.28411.2686-0.02110.0611-0.408-0.1447-0.07250.020.42350.06560.0540.38440.04650.0350.1346-0.04770.302756.3696-39.5802-34.4841
90.65-0.889-0.38232.68330.4640.4056-0.0755-0.0471-0.09780.11140.0784-0.3950.2450.22940.02650.24440.0987-0.00430.26580.00340.268765.1538-26.2191-23.398
100.6919-0.4192-0.02981.565-0.190.73630.0014-0.0091-0.0834-0.1468-0.0943-0.03790.19660.0280.08770.18390.06060.00910.1445-0.01090.156255.1021-21.6852-31.2523
111.9745-0.59711.00422.6225-0.40922.70940.0058-0.1021-0.18370.1033-0.1538-0.54740.17640.40220.08830.21380.1020.00850.30280.06170.29669.7876-14.3608-33.3872
120.58420.1475-0.23141.7049-0.21560.66260.03720.0343-0.0961-0.0843-0.1416-0.06930.13330.01290.10480.17260.06920.01050.1579-0.00090.153155.9632-17.3338-31.1403
133.0106-0.0879-0.45152.9061-0.58830.1922-0.0978-0.7591-0.09520.8057-0.1039-0.02090.10490.45310.16620.51690.04880.02060.36430.00450.244860.4985-32.3762-17.2425
142.0938-0.9830.20670.91960.20460.2230.10460.4695-0.0302-0.6022-0.2924-0.32340.1221-0.0417-0.02260.32130.1680.09140.22950.02480.20763.9709-18.0254-45.3732
153.2325-0.83881.35215.3127-4.24186.0879-0.2043-0.5383-0.38180.45570.2386-1.02881.31450.51180.09470.70050.24110.05160.5557-0.00790.611773.8994-22.3806-32.0265
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 82 )A11 - 82
2X-RAY DIFFRACTION2chain 'A' and (resid 83 through 112 )A83 - 112
3X-RAY DIFFRACTION3chain 'A' and (resid 113 through 164 )A113 - 164
4X-RAY DIFFRACTION4chain 'A' and (resid 165 through 266 )A165 - 266
5X-RAY DIFFRACTION5chain 'A' and (resid 267 through 285 )A267 - 285
6X-RAY DIFFRACTION6chain 'A' and (resid 286 through 306 )A286 - 306
7X-RAY DIFFRACTION7chain 'B' and (resid 11 through 26 )B11 - 26
8X-RAY DIFFRACTION8chain 'B' and (resid 27 through 80 )B27 - 80
9X-RAY DIFFRACTION9chain 'B' and (resid 81 through 118 )B81 - 118
10X-RAY DIFFRACTION10chain 'B' and (resid 119 through 164 )B119 - 164
11X-RAY DIFFRACTION11chain 'B' and (resid 165 through 197 )B165 - 197
12X-RAY DIFFRACTION12chain 'B' and (resid 198 through 266 )B198 - 266
13X-RAY DIFFRACTION13chain 'B' and (resid 267 through 285 )B267 - 285
14X-RAY DIFFRACTION14chain 'B' and (resid 286 through 298 )B286 - 298
15X-RAY DIFFRACTION15chain 'B' and (resid 299 through 315 )B299 - 315

+
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