[English] 日本語
Yorodumi
- PDB-6xjm: Biuret Hydrolase (BiuH) from Rhodococcus sp. Mel C169S bound with... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6xjm
TitleBiuret Hydrolase (BiuH) from Rhodococcus sp. Mel C169S bound with biuret
ComponentsBiuret hydrolase
KeywordsHYDROLASE / TrtA / BiuH / triuret / biuret / cysteine hydrolase / nitrogen
Function / homology: / Isochorismatase-like / Isochorismatase-like superfamily / Isochorismatase domain / hydrolase activity / dicarbonimidic diamide / Biuret hydrolase
Function and homology information
Biological speciesRhodococcus sp. Mel (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
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: Biuret hydrolase
B: Biuret hydrolase
C: Biuret hydrolase
D: Biuret hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,5908
Polymers104,1774
Non-polymers4124
Water7,314406
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, dimer of dimers
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11850 Å2
ΔGint-29 kcal/mol
Surface area26780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.290, 103.340, 133.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Biuret hydrolase


Mass: 26044.336 Da / Num. of mol.: 4 / Mutation: C169S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus sp. Mel (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H8ZKV9
#2: Chemical
ChemComp-C5J / dicarbonimidic diamide


Mass: 103.080 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H5N3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: 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: 2.03 Å3/Da / Density % sol: 39.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 1uL 5 mg/mL protein + 1uL 20% w/v PEG3350, 0.2M MgCl2, 20mM Biuret pH 5.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.99184 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99184 Å / Relative weight: 1
ReflectionResolution: 2.05→81.8 Å / Num. obs: 102760 / % possible obs: 99.7 % / Redundancy: 4.25 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 8.42
Reflection shellResolution: 2.05→2.15 Å / Redundancy: 4.32 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 3.66 / Num. unique obs: 13718 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSBUILT=20200131data reduction
XSCALEBUILT=20200131data scaling
MOLREP11phasing
Coot0.8.9.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 6AZO

6azo


Resolution: 2.05→56.06 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.917 / SU B: 4.695 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.22 / ESU R Free: 0.179
Details: HYDROGENS HAVE BEEN ADDED IN THEIR RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.228 2723 5.036 %
Rwork0.184 --
obs-54076 99.9 %
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 max: 68.7 Å2 / Biso mean: 21.2 Å2 / Biso min: 11.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.012 Å20 Å20 Å2
2---1.262 Å20 Å2
3---0.25 Å2
Refinement stepCycle: final / Resolution: 2.05→56.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6856 0 28 406 7290
Biso mean--19.14 25.27 -
Num. residues----911
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0137035
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176480
X-RAY DIFFRACTIONr_angle_refined_deg1.641.6489587
X-RAY DIFFRACTIONr_angle_other_deg1.3561.58114961
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8015906
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.06120.575348
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.114151073
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9781560
X-RAY DIFFRACTIONr_chiral_restr0.0810.2950
X-RAY DIFFRACTIONr_gen_planes_refined0.0220.098006
X-RAY DIFFRACTIONr_gen_planes_other0.0590.2861502
X-RAY DIFFRACTIONr_nbd_refined0.2040.21418
X-RAY DIFFRACTIONr_nbd_other0.1720.237
X-RAY DIFFRACTIONr_nbtor_refined0.1560.23450
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2467
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.1 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 199 -
Rwork0.209 3725 -
all-3924 -
obs--99.97 %

+
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