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

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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

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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
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

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Components

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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

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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

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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: 2.34 Å3/Da / Density % sol: 47.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 20%PEG3350, 100mM CaCl2

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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

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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 )

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