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- PDB-6dhj: Crystal structures of cyanuric acid hydrolase from Moorella therm... -

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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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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Experiment

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

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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

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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

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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 )

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