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

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Basic information

Entry
Database: PDB / ID: 6bun
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
MALONATE ION / 1,3-PROPANDIOL / Cyanuric acid amidohydrolase
Similarity search - Component
Biological speciesMoorella thermoacetica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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)155,95135
Polymers153,9394
Non-polymers2,01231
Water23,6361312
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, A,B,C,D
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16570 Å2
ΔGint-100 kcal/mol
Surface area46510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.230, 89.330, 199.420
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 , 5 types, 1343 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.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-PDO / 1,3-PROPANDIOL


Mass: 76.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1312 / 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: 47.67 %
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-C / 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: 1.78→89.33 Å / Num. obs: 139408 / % possible obs: 100 % / Redundancy: 7.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 17.3
Reflection shellResolution: 1.78→1.81 Å / Redundancy: 7 % / Rmerge(I) obs: 0.759 / Num. unique obs: 6814 / CC1/2: 0.771 / % possible all: 99.4

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Processing

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

4nq3


Resolution: 1.78→81.524 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.08
RfactorNum. reflection% reflection
Rfree0.1736 1890 1.36 %
Rwork0.1478 --
obs0.1481 139306 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.78→81.524 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10734 0 115 1312 12161
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711045
X-RAY DIFFRACTIONf_angle_d0.80414922
X-RAY DIFFRACTIONf_dihedral_angle_d13.5116775
X-RAY DIFFRACTIONf_chiral_restr0.0581752
X-RAY DIFFRACTIONf_plane_restr0.0051976
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.82810.27221340.240810399X-RAY DIFFRACTION100
1.8281-1.88190.23491400.204410452X-RAY DIFFRACTION100
1.8819-1.94270.21831630.175810488X-RAY DIFFRACTION100
1.9427-2.01210.21021400.165410453X-RAY DIFFRACTION100
2.0121-2.09270.17711440.15910494X-RAY DIFFRACTION100
2.0927-2.18790.1971570.153210501X-RAY DIFFRACTION100
2.1879-2.30330.16691480.144110502X-RAY DIFFRACTION100
2.3033-2.44760.15741510.141410515X-RAY DIFFRACTION100
2.4476-2.63660.19231430.145310567X-RAY DIFFRACTION100
2.6366-2.9020.17471540.148310591X-RAY DIFFRACTION100
2.902-3.32190.17711480.142210615X-RAY DIFFRACTION100
3.3219-4.18520.14871310.124810742X-RAY DIFFRACTION100
4.1852-81.610.14161370.140111097X-RAY DIFFRACTION100
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)
10.99420.0864-0.13631.088-0.30771.5869-0.0048-0.1637-0.05430.17940.0027-0.01210.04850.0242-0.02050.10260.0062-0.00160.08560.00220.090712.955-5.904758.7935
21.9328-1.20771.08123.1498-1.56352.3649-0.0607-0.08140.22560.14770.0128-0.0755-0.22250.04530.0840.1093-0.02910.00160.0911-0.03240.138820.455513.504253.4598
31.1721-0.3040.08661.0488-0.15280.8490.0165-0.02120.0920.0516-0.0238-0.1795-0.05040.15650.01250.0966-0.0173-0.00950.1256-0.01070.139727.98515.834950.7684
41.08430.1380.03190.7391-0.23321.67990.00960.0109-0.0948-0.0197-0.0304-0.13090.09470.20060.05130.08290.02490.00830.1044-0.01480.128628.1024-6.971342.826
53.8143-0.9627-0.0081.08640.22132.00920.0418-0.07950.05960.0833-0.00850.1124-0.0759-0.2323-0.03470.12520.01380.0120.0872-0.01710.1521-15.494211.152949.2009
63.6499-0.9651-1.87331.29270.2693.3565-0.1218-0.2372-0.14170.14890.08650.11350.17040.06220.04130.1158-0.0018-0.00290.0739-0.00040.1325-8.3281-0.011549.7525
71.9376-0.3690.02820.7399-0.09250.9411-0.0459-0.1395-0.04060.02220.02270.1989-0.033-0.24530.00870.10710.0138-0.00520.1407-0.02470.1599-19.11965.451242.2345
83.2641-2.09010.18753.7684-0.29141.6706-0.05730.0256-0.33810.11110.02860.24180.3221-0.09650.01690.1866-0.04770.00480.1277-0.00630.1812-15.3557-14.513137.3658
93.3726-0.93650.12193.0664-0.31952.7544-0.03070.2331-0.2367-0.0944-0.06050.1930.3697-0.13020.05490.175-0.0278-0.0150.1203-0.02520.1619-15.0938-11.885129.0826
101.4631-0.066-0.42580.68260.10861.3750.02460.12490.0771-0.0733-0.00140.1487-0.0486-0.1313-0.02540.11620.0159-0.03810.1150.01310.1327-13.91576.062526.8857
111.3292-0.4335-0.46311.11720.13781.3520.05610.2982-0.0018-0.3226-0.0379-0.16940.1070.2092-0.06160.24030.04420.07310.281-0.03010.13730.7066-11.27279.3156
124.7531-1.67880.08832.16890.23061.56010.08480.4168-0.2492-0.276-0.08170.12040.2259-0.02920.02740.2933-0.01980.01320.2153-0.0730.135412.502-22.583810.3435
132.4951-0.60940.28723.3244-0.19992.1922-0.03790.1322-0.2854-0.08750.05590.12160.3415-0.1373-0.0070.221-0.01350.0210.1623-0.05280.145512.8602-25.37618.381
140.91790.0452-0.53550.85590.30731.7554-0.02020.0714-0.0811-0.08880.0603-0.12710.18880.2217-0.02730.17070.05810.01650.1549-0.02910.140627.2767-19.204527.3895
150.9781-0.3271-0.30841.4487-0.10741.84390.15310.45670.2042-0.5796-0.0861-0.2097-0.22530.00380.04570.39130.03760.07430.30910.09080.151611.566812.42521.4198
162.38310.74470.18682.21840.5473.35540.20220.10110.2701-0.13560.2217-0.9166-0.5680.7718-0.12520.3746-0.13030.11050.3299-0.03040.593519.969228.379617.251
171.0731-0.1437-0.33581.5288-0.14052.19790.07350.27170.2702-0.3163-0.01330.0186-0.2762-0.1137-0.01050.20570.0314-0.00110.16190.07290.17970.394919.281716.2809
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:118 )A1 - 118
2X-RAY DIFFRACTION2( CHAIN A AND RESID 119:184 )A119 - 184
3X-RAY DIFFRACTION3( CHAIN A AND RESID 185:266 )A185 - 266
4X-RAY DIFFRACTION4( CHAIN A AND RESID 267:367 )A267 - 367
5X-RAY DIFFRACTION5( CHAIN B AND RESID 0:30 )B0 - 30
6X-RAY DIFFRACTION6( CHAIN B AND RESID 31:77 )B31 - 77
7X-RAY DIFFRACTION7( CHAIN B AND RESID 78:118 )B78 - 118
8X-RAY DIFFRACTION8( CHAIN B AND RESID 119:184 )B119 - 184
9X-RAY DIFFRACTION9( CHAIN B AND RESID 185:239 )B185 - 239
10X-RAY DIFFRACTION10( CHAIN B AND RESID 240:367 )B240 - 367
11X-RAY DIFFRACTION11( CHAIN C AND RESID 1:118 )C1 - 118
12X-RAY DIFFRACTION12( CHAIN C AND RESID 119:184 )C119 - 184
13X-RAY DIFFRACTION13( CHAIN C AND RESID 185:239 )C185 - 239
14X-RAY DIFFRACTION14( CHAIN C AND RESID 240:367 )C240 - 367
15X-RAY DIFFRACTION15( CHAIN D AND RESID 1:118 )D1 - 118
16X-RAY DIFFRACTION16( CHAIN D AND RESID 119:239 )D119 - 239
17X-RAY DIFFRACTION17( CHAIN D AND RESID 240:367 )D240 - 367

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