[English] 日本語
Yorodumi
- PDB-6xje: Triuret Hydrolase (TrtA) from Herbaspirillum sp. BH-1 C162S bound... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6xje
TitleTriuret Hydrolase (TrtA) from Herbaspirillum sp. BH-1 C162S bound with triuret
ComponentsCysteine hydrolase
KeywordsHYDROLASE / TrtA / triuret / biuret / cysteine hydrolase / nitrogen
Function / homology
Function and homology information


amide catabolic process / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / protein homodimerization activity / identical protein binding
Similarity search - Function
Isochorismatase-like / Isochorismatase-like superfamily / Isochorismatase family
Similarity search - Domain/homology
tricarbonodiimidic diamide / Triuret hydrolase TrtA
Similarity search - Component
Biological speciesHerbaspirillum sp. BH-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsTassoulas, L.T. / Elias, M.H. / Wackett, L.P.
Funding support United States, 2items
OrganizationGrant numberCountry
United States Department of Agriculture (USDA)2019-67019-29403 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5T32GM008347-28 United States
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Discovery of an ultraspecific triuret hydrolase (TrtA) establishes the triuret biodegradation pathway.
Authors: Tassoulas, L.J. / Elias, M.H. / Wackett, L.P.
History
DepositionJun 23, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 21, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 18, 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: Cysteine hydrolase
B: Cysteine hydrolase
C: Cysteine hydrolase
D: Cysteine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,49510
Polymers96,7874
Non-polymers7096
Water7,314406
1
A: Cysteine hydrolase
B: Cysteine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7485
Polymers48,3932
Non-polymers3543
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-9 kcal/mol
Surface area16370 Å2
MethodPISA
2
C: Cysteine hydrolase
D: Cysteine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7485
Polymers48,3932
Non-polymers3543
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-8 kcal/mol
Surface area16460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.530, 114.440, 142.930
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Cysteine hydrolase / triuret hydrolase


Mass: 24196.664 Da / Num. of mol.: 4 / Mutation: C162S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Herbaspirillum sp. BH-1 (bacteria) / Gene: HBH1_00246 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2N6JFX7
#2: Chemical
ChemComp-TIU / tricarbonodiimidic diamide


Mass: 146.105 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H6N4O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 406 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1 uL 20 mg/mL protein + 1 uL 24% w/v PEG6000, 0.1 M Bis-Tris propane, 1 mM triuret, pH 8

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 27, 2018
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03332 Å / Relative weight: 1
ReflectionResolution: 1.45→60.62 Å / Num. obs: 150183 / % possible obs: 100 % / Redundancy: 7.47 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 20.99
Reflection shellResolution: 1.45→1.55 Å / Redundancy: 7.21 % / Rmerge(I) obs: 0.547 / Mean I/σ(I) obs: 3.97 / Num. unique obs: 26952 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSBUILT=20180409data reduction
XDSBUILT=20180409data scaling
MOLREP11phasing
Coot0.8.9.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6XIX

6xix


Resolution: 1.45→60.616 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.093 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.063
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1898 7510 5.001 %
Rwork0.172 142673 -
all0.173 --
obs-150183 99.957 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 19.158 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å2-0 Å2-0 Å2
2---0.549 Å20 Å2
3---0.629 Å2
Refinement stepCycle: LAST / Resolution: 1.45→60.616 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6698 0 48 406 7152
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0136994
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176606
X-RAY DIFFRACTIONr_angle_refined_deg1.8731.6499521
X-RAY DIFFRACTIONr_angle_other_deg1.5941.57515274
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3675902
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.70621.003369
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.733151140
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3241565
X-RAY DIFFRACTIONr_chiral_restr0.1010.2913
X-RAY DIFFRACTIONr_gen_planes_refined0.020.027984
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021463
X-RAY DIFFRACTIONr_nbd_refined0.2190.21244
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.26183
X-RAY DIFFRACTIONr_nbtor_refined0.1640.23482
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.23158
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2315
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1640.210
X-RAY DIFFRACTIONr_nbd_other0.2250.260
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1420.27
X-RAY DIFFRACTIONr_mcbond_it1.7031.8233578
X-RAY DIFFRACTIONr_mcbond_other1.6961.8223577
X-RAY DIFFRACTIONr_mcangle_it2.3562.7294490
X-RAY DIFFRACTIONr_mcangle_other2.3592.734491
X-RAY DIFFRACTIONr_scbond_it3.0832.1593416
X-RAY DIFFRACTIONr_scbond_other3.0832.1593417
X-RAY DIFFRACTIONr_scangle_it4.5463.125031
X-RAY DIFFRACTIONr_scangle_other4.5463.125032
X-RAY DIFFRACTIONr_lrange_it5.31822.2547539
X-RAY DIFFRACTIONr_lrange_other5.31822.2587540
X-RAY DIFFRACTIONr_ncsr_local_group_10.0810.056956
X-RAY DIFFRACTIONr_ncsr_local_group_20.0790.056935
X-RAY DIFFRACTIONr_ncsr_local_group_30.10.056849
X-RAY DIFFRACTIONr_ncsr_local_group_40.0870.056838
X-RAY DIFFRACTIONr_ncsr_local_group_50.0840.056856
X-RAY DIFFRACTIONr_ncsr_local_group_60.0930.056811
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.45-1.4880.3155490.288104250.289109760.8770.88299.98180.257
1.488-1.5280.2975360.257101760.259107140.8860.90199.98130.228
1.528-1.5730.2425220.22699160.227104400.9190.92299.98080.198
1.573-1.6210.2265060.19796240.198101300.9290.9341000.173
1.621-1.6740.2124920.18293500.18498430.940.94699.98980.16
1.674-1.7330.2124740.17990070.18194810.9430.9521000.16
1.733-1.7980.2094600.17687400.17892010.9420.95499.98910.16
1.798-1.8720.1954430.17384110.17488550.9490.95799.98870.161
1.872-1.9550.1934250.17780720.17884990.9540.95999.97650.17
1.955-2.050.214080.17777630.17981730.9470.95799.97550.173
2.05-2.1610.2073880.17473700.17677580.9510.9571000.176
2.161-2.2920.1923670.16569600.16673280.9570.96499.98640.171
2.292-2.450.1723460.1665850.16169340.9650.96799.95670.171
2.45-2.6460.1643220.15961090.15964350.9680.96899.93780.174
2.646-2.8980.1842980.16556730.16659740.9590.96299.94980.184
2.898-3.2390.1752720.1751680.1754450.9610.96299.90820.194
3.239-3.7380.1722400.16145530.16148000.9660.96899.85420.188
3.738-4.5740.1482050.14439010.14541120.9760.97599.85410.178
4.574-6.450.1861620.16930770.1732420.970.97699.90750.215
6.45-60.6160.206950.18117940.18319070.9680.96899.05610.246

+
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