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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6dhj
TitleCrystal structures of cyanuric acid hydrolase from Moorella thermoacetica
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
CITRIC ACID / Cyanuric acid amidohydrolase
Similarity search - Component
Biological speciesMoorella thermoacetica ATCC 39073 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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
DepositionMay 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
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
E: Cyanuric acid amidohydrolase
F: Cyanuric acid amidohydrolase
G: Cyanuric acid amidohydrolase
H: Cyanuric acid amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)316,62216
Polymers315,0858
Non-polymers1,5378
Water00
1
A: Cyanuric acid amidohydrolase
E: Cyanuric acid amidohydrolase
F: Cyanuric acid amidohydrolase
H: Cyanuric acid amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,3118
Polymers157,5434
Non-polymers7684
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11500 Å2
ΔGint-16 kcal/mol
Surface area50640 Å2
MethodPISA
2
B: Cyanuric acid amidohydrolase
C: Cyanuric acid amidohydrolase
D: Cyanuric acid amidohydrolase
G: Cyanuric acid amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,3118
Polymers157,5434
Non-polymers7684
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11210 Å2
ΔGint-13 kcal/mol
Surface area50460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.905, 164.563, 202.872
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Cyanuric acid amidohydrolase / CAH


Mass: 39385.625 Da / Num. of mol.: 8
Mutation: C46S, G53C, Q103A, E104A, K107A, C162A, C218V, E235C, K279I, K280R, F281S, E288D, L290M, A291D, K292R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moorella thermoacetica ATCC 39073 (bacteria)
Strain: ATCC 39073 / JCM 9320 / Gene: Moth_2120 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2RGM7, cyanuric acid amidohydrolase
#2: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H8O7
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M tri-ammonium citrate, 20 %w/v PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.2→164.56 Å / Num. obs: 56567 / % possible obs: 98.6 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 10.3
Reflection shellResolution: 3.2→3.29 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 4674 / CC1/2: 0.39 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CWJ

6cwj


Resolution: 3.2→127.803 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2497 2804 5.09 %
Rwork0.2077 --
obs0.2099 55081 95.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→127.803 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21462 0 104 0 21566
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00521813
X-RAY DIFFRACTIONf_angle_d0.96529537
X-RAY DIFFRACTIONf_dihedral_angle_d14.43613393
X-RAY DIFFRACTIONf_chiral_restr0.0573507
X-RAY DIFFRACTIONf_plane_restr0.0063898
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)
12.93521.05760.02310.9244-0.96982.22040.07620.2110.04821.1743-0.3739-0.7269-0.60960.515800.9334-0.0433-0.06490.85160.15120.8437-18.51326.1676-15.633
21.85660.10910.54041.1642-0.43272.099-0.71830.8809-1.1426-0.4513-0.3622-1.43350.7270.5606-0.11730.8986-0.08980.52691.25020.08670.7451-20.667220.5302-36.4085
30.36610.2685-0.2052.4355-0.27590.5193-0.49580.8193-0.0337-0.97290.2472-0.65090.4874-0.6429-0.01091.0108-0.0410.23561.37160.16030.6062-32.982921.7965-31.6149
41.7687-0.27280.54231.76351.01150.9131-0.52690.52450.33610.21410.44280.5276-0.0552-0.5188-0.12260.82380.06870.15841.12740.26740.501-36.492232.6601-25.5642
50.86290.9672-0.77512.13290.40312.5017-0.1741-0.2601-0.5288-0.48680.3305-0.10910.3248-0.33420.00010.78270.0435-0.02950.833-0.07651.3156-64.4141-23.1711-18.5068
61.52630.9324-1.21132.211-0.14623.3243-0.3940.3514-0.0481-0.76140.14070.61-0.40530.0551-01.1757-0.0202-0.09561.0063-0.20540.9195-56.9075-8.4833-34.9181
72.35410.58831.54192.857-0.71771.296-0.1223-0.3707-0.164-0.05230.0037-0.1206-0.30070.080400.79630.05990.07340.7285-0.03510.9222-51.2941-8.8214-16.6302
82.3026-0.1205-0.23911.92291.9321.6649-0.17260.27820.1748-1.06980.47490.25210.0635-0.14130.02611.029-0.022-0.05470.9133-0.2121.2579-56.0094-49.1127-30.4028
91.10230.36420.10860.20750.92523.64540.1075-0.2842-1.2333-0.2472-0.32860.5801-0.1029-0.1185-0.00011.0570.16620.0891.1563-0.00031.488-47.4339-56.5223-8.74
100.89170.5724-0.67183.1257-1.67951.0133-0.3587-0.0027-0.5236-0.6901-0.0426-0.39390.76110.355401.09770.16580.26710.9706-0.22831.4356-37.8643-52.6762-26.5514
110.8339-0.13730.09250.1503-0.12992.7916-0.15450.4563-0.6969-0.22690.1163-0.9268-0.36470.756400.7316-0.13150.18951.0083-0.07861.3865-15.3096-12.3963-6.6963
123.1169-0.72890.26661.3252-1.64212.85650.0123-0.4941-0.8120.4665-0.2386-0.2520.35670.1413-00.9151-0.0528-0.00380.88960.13841.3751-23.7383-24.700511.2273
133.04840.48421.39320.7951-0.6261.6634-0.1447-0.1366-0.43760.1839-0.00120.0205-0.0128-0.24700.838-0.02870.12940.76430.10141.0693-33.515-12.43940.1912
140.85530.6607-0.47591.7643-0.68310.58410.1247-0.1632-0.53660.2658-0.1368-0.2836-0.11780.302201.2175-0.1578-0.25921.27810.10181.18182.281746.5757-16.1149
157.59-1.8884-1.51840.96950.77380.6742-0.1255-1.739-1.89590.9124-0.7499-0.0272-1.1910.1954-0.68062.2306-0.3283-0.15411.8020.13230.7061-10.019657.40640.0324
161.1067-1.4367-0.4162.4528-0.53621.58460.18410.12720.71410.9595-0.3371-0.0512-1.12460.12150.01221.5966-0.2518-0.16180.962-0.08320.7804-5.651264.811-17.2168
173.1032-2.097-0.79631.621-0.44275.34660.48290.0422.0395-0.43160.57341.1592-1.798-0.46152.48690.67240.67810.15011.38641.25472.367-53.223462.6184-33.498
182.42010.4119-0.75311.1113-0.49082.11540.3070.6692.83681.14430.30081.4703-0.8235-0.62331.51951.62150.40110.80231.25080.55732.5273-51.679564.2447-14.5559
190.1178-0.0566-0.94331.09380.20483.3450.003-0.26680.4661.03820.37060.87150.4789-0.3060.02331.23940.25660.38171.17160.2581.4903-49.750548.7921-13.5841
201.8488-0.34890.81722.02380.29420.29530.0290.14011.42630.0476-0.36440.58480.0830.3348-0.18721.16380.20790.52111.20240.39971.2198-47.345447.3566-20.1804
210.45790.14991.09221.1116-0.10422.3187-0.267-0.4649-0.212-0.4359-0.0833-0.3526-0.40921.01-0.24280.7806-0.01660.49921.6796-0.26661.6559-5.6313-32.6383-25.7058
222.9082-1.50631.45260.7936-0.09752.3176-0.817-0.79661.4692-1.83020.4076-2.6857-1.49752.2612-0.89641.5276-0.16870.79431.587-0.00522.0756-12.4196-18.6287-42.5419
230.4-0.38130.40390.1591-0.23270.2450.06710.6411-0.0461-2.67790.0034-0.4095-1.11740.36402.1153-0.02130.44172.10550.16651.6515-19.7967-24.3969-45.3042
240.1905-0.1237-0.13751.0786-0.9562.6715-0.10421.9566-0.3742-1.4130.0040.07670.340.1703-0.21521.17890.20270.78031.4122-0.33971.2367-19.8645-41.812-37.9302
250.70650.09170.05141.2760.94050.63790.5618-0.48861.778-1.7507-0.3608-1.2991-0.40680.7772-0.01141.11690.2090.42341.4698-0.09551.1545-21.3125-38.9939-34.1458
263.08340.18980.97023.5686-0.68743.404-0.12250.28840.27390.14620.06931.1295-0.7488-0.5197-0.00381.26340.20.11010.93630.20160.9554-28.81774.5452-48.3379
270.4839-0.37610.0260.77960.46480.46870.41380.4603-0.0478-0.8181-0.22260.75150.8823-0.08060.00011.61240.13460.07211.36350.0061.0265-26.927953.6558-56.4449
283.6328-1.6840.93142.06831.52412.86440.08540.55550.159-0.015-0.28620.0436-0.34280.3894-01.2699-0.1393-0.01560.99930.06460.7339-14.370767.5667-43.0749
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 101 )
2X-RAY DIFFRACTION2chain 'A' and (resid 102 through 204 )
3X-RAY DIFFRACTION3chain 'A' and (resid 205 through 281 )
4X-RAY DIFFRACTION4chain 'A' and (resid 282 through 370 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 101 )
6X-RAY DIFFRACTION6chain 'B' and (resid 102 through 227 )
7X-RAY DIFFRACTION7chain 'B' and (resid 228 through 368 )
8X-RAY DIFFRACTION8chain 'C' and (resid 1 through 118 )
9X-RAY DIFFRACTION9chain 'C' and (resid 119 through 227 )
10X-RAY DIFFRACTION10chain 'C' and (resid 228 through 367 )
11X-RAY DIFFRACTION11chain 'D' and (resid 1 through 101 )
12X-RAY DIFFRACTION12chain 'D' and (resid 102 through 227 )
13X-RAY DIFFRACTION13chain 'D' and (resid 228 through 369 )
14X-RAY DIFFRACTION14chain 'E' and (resid 1 through 118 )
15X-RAY DIFFRACTION15chain 'E' and (resid 119 through 204 )
16X-RAY DIFFRACTION16chain 'E' and (resid 205 through 369 )
17X-RAY DIFFRACTION17chain 'F' and (resid 1 through 77 )
18X-RAY DIFFRACTION18chain 'F' and (resid 78 through 204 )
19X-RAY DIFFRACTION19chain 'F' and (resid 205 through 322 )
20X-RAY DIFFRACTION20chain 'F' and (resid 323 through 368 )
21X-RAY DIFFRACTION21chain 'G' and (resid 1 through 118 )
22X-RAY DIFFRACTION22chain 'G' and (resid 119 through 184 )
23X-RAY DIFFRACTION23chain 'G' and (resid 185 through 239 )
24X-RAY DIFFRACTION24chain 'G' and (resid 240 through 322 )
25X-RAY DIFFRACTION25chain 'G' and (resid 323 through 367 )
26X-RAY DIFFRACTION26chain 'H' and (resid 1 through 162 )
27X-RAY DIFFRACTION27chain 'H' and (resid 163 through 216 )
28X-RAY DIFFRACTION28chain 'H' and (resid 217 through 368 )

+
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