[English] 日本語
Yorodumi
- PDB-6bup: Crystal structures of cyanuric acid hydrolase from Moorella therm... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6bup
TitleCrystal structures of cyanuric acid hydrolase from Moorella thermoacetica complexed with cyanuric acid
ComponentsCyanuric acid amidohydrolase
KeywordsHYDROLASE / Cyanuric acid hydrolase
Function / homology
Function and homology information


cyanuric acid amidohydrolase / cyanuric acid amidohydrolase activity / atrazine catabolic process / metal ion binding
Similarity search - Function
Cyanuric acid hydrolase/Barbituras, RU C / Cyanuric acid hydrolase/Barbiturase, RU A / Cyanuric acid hydrolase/Barbiturase / Cyanuric acid hydrolase/Barbiturase, repeating unit B / Cyanuric acid hydrolase/Barbiturase, repeating unit C / Cyanuric acid hydrolase/Barbiturase, repeating unit A / Amidohydrolase ring-opening protein (Amido_AtzD_TrzD) / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
MALONATE ION / 1,3-PROPANDIOL / DI(HYDROXYETHYL)ETHER / 1,3,5-triazine-2,4,6-triol / Cyanuric acid amidohydrolase
Similarity search - Component
Biological speciesMoorella thermoacetica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsShi, K. / Aihara, H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM095558 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118047 United States
CitationJournal: Plos One / Year: 2019
Title: Crystal structures of Moorella thermoacetica cyanuric acid hydrolase reveal conformational flexibility and asymmetry important for catalysis.
Authors: Shi, K. / Cho, S. / Aukema, K.G. / Lee, T. / Bera, A.K. / Seffernick, J.L. / Wackett, L.P. / Aihara, H.
History
DepositionDec 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 15, 2020Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.4Oct 4, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Cyanuric acid amidohydrolase
B: Cyanuric acid amidohydrolase
C: Cyanuric acid amidohydrolase
D: Cyanuric acid amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,94430
Polymers153,9394
Non-polymers2,00526
Water15,241846
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14930 Å2
ΔGint-48 kcal/mol
Surface area46350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.070, 89.420, 198.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Cyanuric acid amidohydrolase / CAH


Mass: 38484.652 Da / Num. of mol.: 4
Mutation: Q102A, E102A, K107A, L279I, K280R, F281S, E288D, L290M, A291D, K292R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moorella thermoacetica (strain ATCC 39073 / JCM 9320) (bacteria)
Strain: ATCC 39073 / JCM 9320 / Gene: Moth_2120 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2RGM7, cyanuric acid amidohydrolase

-
Non-polymers , 7 types, 872 molecules

#2: Chemical
ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H2O4
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-PDO / 1,3-PROPANDIOL


Mass: 76.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-WDL / 1,3,5-triazine-2,4,6-triol / Cyanuric Acid


Mass: 129.074 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H3N3O3
#7: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 846 / 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: 2.34 Å3/Da / Density % sol: 47.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 20%PEG3350, 100mM CaCl2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.88→99.28 Å / Num. obs: 117898 / % possible obs: 100 % / Redundancy: 13.9 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 6.7
Reflection shellResolution: 1.88→1.91 Å / Redundancy: 1.5 % / Rmerge(I) obs: 1.249 / Num. unique obs: 5831 / CC1/2: 0.52 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
PHENIX(1.13rc2_2981: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NQ3

4nq3


Resolution: 1.88→99.275 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.6
RfactorNum. reflection% reflection
Rfree0.1808 2024 1.72 %
Rwork0.148 --
obs0.1485 117801 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.88→99.275 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10744 0 133 846 11723
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0110993
X-RAY DIFFRACTIONf_angle_d0.98714843
X-RAY DIFFRACTIONf_dihedral_angle_d15.5196711
X-RAY DIFFRACTIONf_chiral_restr0.0611742
X-RAY DIFFRACTIONf_plane_restr0.0061957
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.9270.31031490.26618174X-RAY DIFFRACTION100
1.927-1.97910.26731350.22778201X-RAY DIFFRACTION100
1.9791-2.03740.24681580.20058163X-RAY DIFFRACTION100
2.0374-2.10320.22691490.17978151X-RAY DIFFRACTION100
2.1032-2.17830.22721340.16338237X-RAY DIFFRACTION100
2.1783-2.26560.18511550.15188164X-RAY DIFFRACTION100
2.2656-2.36870.19221250.14068265X-RAY DIFFRACTION100
2.3687-2.49360.18091540.14238205X-RAY DIFFRACTION100
2.4936-2.64980.18141280.13938254X-RAY DIFFRACTION100
2.6498-2.85440.20061400.1398264X-RAY DIFFRACTION100
2.8544-3.14170.17311560.14558289X-RAY DIFFRACTION100
3.1417-3.59630.15521430.13278326X-RAY DIFFRACTION100
3.5963-4.5310.1381470.12528420X-RAY DIFFRACTION100
4.531-99.41370.18331510.15118664X-RAY DIFFRACTION99
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)
11.59470.07120.51152.69351.20194.3854-0.0048-0.22010.03250.30270.0341-0.0780.02340.0281-0.03670.1503-0.00590.00250.15250.00210.182230.06446.018556.987
22.0323-0.0368-0.18292.8130.41812.1891-0.041-0.3541-0.07130.5720.02130.20840.2008-0.18060.04590.2156-0.00810.01340.27330.0470.192818.1476-5.056861.0724
31.22030.05790.09921.1725-0.03981.43780.0144-0.0839-0.050.08060.00520.21520.0281-0.2528-0.00620.1524-0.01470.0080.21010.01420.20914.1936-1.24347.3827
41.538-0.22710.19381.0932-0.22722.2721-0.0286-0.1141-0.07470.089-0.0368-0.23150.03110.33180.07480.15850.0085-0.00320.17160.03280.244854.4381-4.30546.9276
52.2055-0.45050.45453.29-1.11493.5991-0.08980.09690.38530.2355-0.0831-0.2965-0.81510.24010.16150.3484-0.0652-0.02060.19680.03370.256955.735613.619433.5132
61.9120.05840.9311.0097-0.422.26250.07670.2159-0.2321-0.154-0.0782-0.20930.15750.2891-0.01320.21480.03020.06040.2205-0.00470.253954.429-5.859326.8588
72.6595-0.5961.0011.8033-0.65282.65320.02070.4830.0911-0.3980.05230.2503-0.0266-0.3089-0.07880.2755-0.0028-0.06240.3570.04820.20499.469411.62169.3555
83.0364-0.6062-0.82092.08340.29582.1110.02970.44530.377-0.3206-0.0072-0.107-0.2694-0.0134-0.00450.2839-0.0181-0.01680.26270.0730.205727.595424.05613.7462
91.94720.16261.29281.137-0.57042.746-0.03040.05680.1745-0.06830.06110.1596-0.1862-0.3064-0.04330.22280.05390.00170.20040.02190.194513.134719.466927.4535
101.5693-0.74420.15172.47670.65152.59120.19560.7829-0.3723-0.7788-0.1560.27060.3569-0.016-0.03110.52680.0345-0.07450.5011-0.14360.268528.7737-12.22431.417
113.94480.22790.19993.5565-0.80123.88470.06280.2457-0.4572-0.11650.30391.15010.4262-0.8014-0.35570.5475-0.1011-0.05450.45370.04050.79220.4253-28.099917.2163
121.448-0.3739-0.04132.79380.73494.52790.10280.3782-0.3852-0.4313-0.063-0.01640.38020.0758-0.04170.28260.0316-0.0020.234-0.09620.307340.1987-19.111216.1348
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 92 )
2X-RAY DIFFRACTION2chain 'A' and (resid 93 through 146 )
3X-RAY DIFFRACTION3chain 'A' and (resid 147 through 367 )
4X-RAY DIFFRACTION4chain 'B' and (resid 0 through 118 )
5X-RAY DIFFRACTION5chain 'B' and (resid 119 through 239 )
6X-RAY DIFFRACTION6chain 'B' and (resid 240 through 367 )
7X-RAY DIFFRACTION7chain 'C' and (resid 0 through 118 )
8X-RAY DIFFRACTION8chain 'C' and (resid 119 through 239 )
9X-RAY DIFFRACTION9chain 'C' and (resid 240 through 367 )
10X-RAY DIFFRACTION10chain 'D' and (resid 1 through 118 )
11X-RAY DIFFRACTION11chain 'D' and (resid 119 through 239 )
12X-RAY DIFFRACTION12chain 'D' and (resid 240 through 367 )

+
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