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

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Basic information

Entry
Database: PDB / ID: 6buq
TitleCrystal structures of cyanuric acid hydrolase from Moorella thermoacetica complexed with barbituric 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
BARBITURIC ACID / MALONATE ION / 1,3-PROPANDIOL / DI(HYDROXYETHYL)ETHER / 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 1.3Oct 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 / _struct_conn.ptnr2_label_seq_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)155,47025
Polymers153,9394
Non-polymers1,53121
Water14,358797
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14610 Å2
ΔGint-59 kcal/mol
Surface area45630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.050, 89.770, 198.710
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 / Barbiturase


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 , 8 types, 818 molecules

#2: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / 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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-PDO / 1,3-PROPANDIOL


Mass: 76.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O2
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-BR8 / BARBITURIC ACID


Mass: 128.086 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H4N2O3
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 797 / 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: 2.35 Å3/Da / Density % sol: 47.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / 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→89.87 Å / Num. obs: 117905 / % possible obs: 99.5 % / Redundancy: 4.4 % / CC1/2: 0.543 / Rmerge(I) obs: 0.085 / Net I/σ(I): 11
Reflection shellResolution: 1.88→1.91 Å / Redundancy: 4.4 % / Rmerge(I) obs: 1.087 / Num. unique obs: 5779 / CC1/2: 0.543 / % possible all: 98.4

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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→39.708 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.92
RfactorNum. reflection% reflection
Rfree0.1816 3792 1.71 %
Rwork0.1558 --
obs0.1562 111097 97.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.88→39.708 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10724 0 93 797 11614
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710984
X-RAY DIFFRACTIONf_angle_d0.77114845
X-RAY DIFFRACTIONf_dihedral_angle_d14.9686729
X-RAY DIFFRACTIONf_chiral_restr0.0541745
X-RAY DIFFRACTIONf_plane_restr0.0051962
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.90380.33541410.32957879X-RAY DIFFRACTION95
1.9038-1.92890.35971450.29628212X-RAY DIFFRACTION98
1.9289-1.95530.30881250.28828183X-RAY DIFFRACTION98
1.9553-1.98320.2491480.26998112X-RAY DIFFRACTION98
1.9832-2.01280.26771460.25548045X-RAY DIFFRACTION97
2.0128-2.04430.29041650.25067989X-RAY DIFFRACTION97
2.0443-2.07780.29721460.24638003X-RAY DIFFRACTION96
2.0778-2.11360.22031260.21268104X-RAY DIFFRACTION98
2.1136-2.1520.20521510.19178201X-RAY DIFFRACTION99
2.152-2.19340.23251230.18478292X-RAY DIFFRACTION99
2.1934-2.23820.21451520.18588147X-RAY DIFFRACTION98
2.2382-2.28680.22041630.17628079X-RAY DIFFRACTION98
2.2868-2.340.18841110.15928158X-RAY DIFFRACTION99
2.34-2.39860.17961510.14898171X-RAY DIFFRACTION98
2.3986-2.46340.18031300.15598094X-RAY DIFFRACTION98
2.4634-2.53590.17421460.14868097X-RAY DIFFRACTION97
2.5359-2.61770.1961180.14358212X-RAY DIFFRACTION99
2.6177-2.71120.16271410.13648202X-RAY DIFFRACTION99
2.7112-2.81980.17531410.14498181X-RAY DIFFRACTION99
2.8198-2.94810.19621350.13998143X-RAY DIFFRACTION98
2.9481-3.10340.14991560.14568036X-RAY DIFFRACTION97
3.1034-3.29780.18681220.13687856X-RAY DIFFRACTION95
3.2978-3.55230.15161500.13538092X-RAY DIFFRACTION97
3.5523-3.90950.17011410.13137992X-RAY DIFFRACTION97
3.9095-4.47450.1431480.1237984X-RAY DIFFRACTION96
4.4745-5.63480.13781200.13137886X-RAY DIFFRACTION95
5.6348-39.71650.1621510.15028052X-RAY DIFFRACTION97
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)
11.62780.05490.22941.9257-0.78642.9411-0.0193-0.2302-0.02370.27890.0331-0.02120.0491-0.0609-0.03540.24470.00190.0020.1968-0.01260.19629.3048-6.085758.3121
21.95260.3088-0.5852.20070.23352.27450.0429-0.4078-0.07950.4027-0.0509-0.17620.17540.16410.02590.24610.0205-0.04210.2250.02510.196220.4945-6.628659.8812
32.0652-1.50970.31325.8965-2.41761.2506-0.1321-0.21440.33570.44750.1281-0.2452-0.35430.0810.08140.3123-0.0205-0.03220.2536-0.08820.294121.879914.589657.4533
41.5766-0.1621-0.02691.4659-0.00771.07630.0216-0.09320.19960.12330.0048-0.1787-0.13120.1489-0.01230.2229-0.0247-0.01010.2251-0.02450.252824.9628.007150.7634
52.1841.0438-1.0394.0376-0.82093.0986-0.0466-0.2204-0.520.0604-0.1094-0.60140.57050.44310.05230.29350.0784-0.05280.27960.00640.370932.2574-14.815950.8808
61.28580.18590.1071.09360.1931.22450.00140.09460.069-0.0452-0.0017-0.15010.02480.16920.00110.20340.02130.00980.2305-0.01230.241726.2533-3.723139.4151
71.15080.01340.05230.84530.32891.3042-0.0123-0.09490.11680.0923-0.05510.2670.0265-0.20140.0650.17460.00290.0120.1783-0.02450.2645-14.90410.080145.1823
83.5352-1.2154-0.18363.90950.53511.47520.02190.1088-0.21170.0537-0.09110.07750.18250.03690.02730.2303-0.0246-0.00360.2026-0.01920.223-12.3914-13.94136.2363
91.7718-0.2076-0.22311.28890.09471.11460.03550.24930.1237-0.164-0.06570.2297-0.0148-0.13030.02380.23730.0114-0.06930.2475-0.00320.2537-14.19780.279527.6287
101.3672-0.0426-0.72091.27560.35821.8840.02170.46730.0121-0.33190.0898-0.3868-0.03690.3398-0.13290.3284-0.00230.11510.4973-0.04710.267432.1609-9.001811.3627
112.2179-0.5144-3.08331.62970.65324.43490.11390.78040.2411-0.66070.0213-0.1888-0.129-0.0716-0.09960.49620.01670.09390.71420.03580.24426.2764-6.57091.7398
121.19280.1722-0.54041.0730.02231.3748-0.11740.6427-0.2209-0.31810.0996-0.12120.30650.14120.04170.40350.02880.07070.5087-0.12720.233224.5598-21.578110.2858
133.718-0.7746-0.1852.36620.33851.8498-0.09350.4364-0.1035-0.30110.07760.14730.1626-0.20510.01160.3972-0.03210.02480.4696-0.08270.189212.0243-20.55112.4042
142.9296-0.33130.12742.57510.14852.16430.0070.3415-0.5257-0.22080.02990.01340.4555-0.18350.03370.3607-0.0250.01640.3804-0.08570.25911.9203-27.542418.158
151.5980.2573-0.40511.15340.40651.6171-0.0890.2558-0.1898-0.11620.0946-0.16660.20240.18920.00270.23770.04830.03210.2514-0.04260.196525.3486-20.006626.0299
160.2478-0.22070.16731.0384-0.34432.22620.10070.80690.3559-0.555-0.0647-0.2237-0.25990.14270.02440.55130.0380.0880.70270.19970.299613.04938.92932.6447
170.9331-0.0950.74092.24920.34034.11590.09960.70070.7285-0.25750.0644-0.3458-0.67220.8215-0.07540.5702-0.13830.13150.67280.24250.677918.815824.902213.3028
181.1013-0.2434-0.23541.4763-0.31662.48650.15820.46080.5252-0.419-0.0741-0.1123-0.38870.01790.00260.41160.04710.02250.34850.18640.41022.92219.831316.8014
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 77 )
2X-RAY DIFFRACTION2chain 'A' and (resid 78 through 118 )
3X-RAY DIFFRACTION3chain 'A' and (resid 119 through 146 )
4X-RAY DIFFRACTION4chain 'A' and (resid 147 through 266 )
5X-RAY DIFFRACTION5chain 'A' and (resid 267 through 300 )
6X-RAY DIFFRACTION6chain 'A' and (resid 301 through 367 )
7X-RAY DIFFRACTION7chain 'B' and (resid 0 through 146 )
8X-RAY DIFFRACTION8chain 'B' and (resid 147 through 184 )
9X-RAY DIFFRACTION9chain 'B' and (resid 185 through 367 )
10X-RAY DIFFRACTION10chain 'C' and (resid 1 through 50 )
11X-RAY DIFFRACTION11chain 'C' and (resid 51 through 77 )
12X-RAY DIFFRACTION12chain 'C' and (resid 78 through 146 )
13X-RAY DIFFRACTION13chain 'C' and (resid 147 through 184 )
14X-RAY DIFFRACTION14chain 'C' and (resid 185 through 216 )
15X-RAY DIFFRACTION15chain 'C' and (resid 217 through 367 )
16X-RAY DIFFRACTION16chain 'D' and (resid 1 through 92 )
17X-RAY DIFFRACTION17chain 'D' and (resid 93 through 216 )
18X-RAY DIFFRACTION18chain 'D' and (resid 217 through 367 )

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