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

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Basic information

Entry
Database: PDB / ID: 6cwj
TitleCrystal structures of cyanuric acid hydrolase from Moorella thermoacetica complexed with 1,3-Acetone Dicarboxylic 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
3-oxopentanedioic acid / ACETATE ION / MALONATE ION / 1,3-PROPANDIOL / Cyanuric acid amidohydrolase
Similarity search - Component
Biological speciesMoorella thermoacetica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.253 Å
AuthorsShi, K. / Aihara, H.
Funding support United States, 3items
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
National Science Foundation (NSF, United States)MCB-1330760 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
DepositionMar 30, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Database references / Category: pdbx_audit_support / struct_ref_seq_dif
Item: _pdbx_audit_support.funding_organization / _struct_ref_seq_dif.details
Revision 1.2Dec 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 1.3Oct 4, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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)154,95217
Polymers153,9394
Non-polymers1,01313
Water10,665592
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12610 Å2
ΔGint-76 kcal/mol
Surface area46390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.140, 88.840, 190.510
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 79 or (resid 80...
21(chain B and (resid 1 through 79 or (resid 80...
31(chain C and (resid 1 through 79 or (resid 80...
41(chain D and (resid 1 through 79 or (resid 80...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETALAALA(chain A and (resid 1 through 79 or (resid 80...AA1 - 792 - 80
12PHEPHEPHEPHE(chain A and (resid 1 through 79 or (resid 80...AA8081
13HISHISVALVAL(chain A and (resid 1 through 79 or (resid 80...AA0 - 3621 - 363
14HISHISVALVAL(chain A and (resid 1 through 79 or (resid 80...AA0 - 3621 - 363
15HISHISVALVAL(chain A and (resid 1 through 79 or (resid 80...AA0 - 3621 - 363
16HISHISVALVAL(chain A and (resid 1 through 79 or (resid 80...AA0 - 3621 - 363
17HISHISVALVAL(chain A and (resid 1 through 79 or (resid 80...AA0 - 3621 - 363
21METMETALAALA(chain B and (resid 1 through 79 or (resid 80...BB1 - 792 - 80
22PHEPHEPHEPHE(chain B and (resid 1 through 79 or (resid 80...BB8081
23HISHISVALVAL(chain B and (resid 1 through 79 or (resid 80...BB0 - 3621 - 363
24HISHISVALVAL(chain B and (resid 1 through 79 or (resid 80...BB0 - 3621 - 363
25HISHISVALVAL(chain B and (resid 1 through 79 or (resid 80...BB0 - 3621 - 363
26HISHISVALVAL(chain B and (resid 1 through 79 or (resid 80...BB0 - 3621 - 363
27HISHISVALVAL(chain B and (resid 1 through 79 or (resid 80...BB0 - 3621 - 363
31METMETALAALA(chain C and (resid 1 through 79 or (resid 80...CC1 - 792 - 80
32PHEPHEPHEPHE(chain C and (resid 1 through 79 or (resid 80...CC8081
33HISHISVALVAL(chain C and (resid 1 through 79 or (resid 80...CC0 - 3621 - 363
34HISHISVALVAL(chain C and (resid 1 through 79 or (resid 80...CC0 - 3621 - 363
35HISHISVALVAL(chain C and (resid 1 through 79 or (resid 80...CC0 - 3621 - 363
36HISHISVALVAL(chain C and (resid 1 through 79 or (resid 80...CC0 - 3621 - 363
37HISHISVALVAL(chain C and (resid 1 through 79 or (resid 80...CC0 - 3621 - 363
41METMETALAALA(chain D and (resid 1 through 79 or (resid 80...DD1 - 792 - 80
42PHEPHEPHEPHE(chain D and (resid 1 through 79 or (resid 80...DD8081
43HISHISVALVAL(chain D and (resid 1 through 79 or (resid 80...DD0 - 3621 - 363
44HISHISVALVAL(chain D and (resid 1 through 79 or (resid 80...DD0 - 3621 - 363
45HISHISVALVAL(chain D and (resid 1 through 79 or (resid 80...DD0 - 3621 - 363
46HISHISVALVAL(chain D and (resid 1 through 79 or (resid 80...DD0 - 3621 - 363
47HISHISVALVAL(chain D and (resid 1 through 79 or (resid 80...DD0 - 3621 - 363

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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: Q103A, E104A, K107A, L279I, K280R, F281S
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 , 6 types, 605 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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-6JN / 3-oxopentanedioic acid


Mass: 146.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H6O5
#6: Chemical ChemComp-PDO / 1,3-PROPANDIOL


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 592 / 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: 2.18 Å3/Da / Density % sol: 43.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: Tascimate, pH5.0. PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97922 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97922 Å / Relative weight: 1
ReflectionResolution: 2.25→95.3 Å / Num. obs: 137972 / % possible obs: 99.5 % / Redundancy: 6.3 % / Biso Wilson estimate: 32.95 Å2 / Rmerge(I) obs: 0.142 / Net I/σ(I): 10.6
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 5.7 % / Rmerge(I) obs: 1.22 / CC1/2: 0.525 / % possible all: 96.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXdev_3082refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BUM

6bum


Resolution: 2.253→95.255 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2236 6021 4.99 %
Rwork0.186 114735 -
obs0.1879 120756 98.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 121.95 Å2 / Biso mean: 43.3092 Å2 / Biso min: 13.93 Å2
Refinement stepCycle: final / Resolution: 2.253→95.255 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10764 0 62 592 11418
Biso mean--46.93 39.86 -
Num. residues----1452
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6645X-RAY DIFFRACTION6.185TORSIONAL
12B6645X-RAY DIFFRACTION6.185TORSIONAL
13C6645X-RAY DIFFRACTION6.185TORSIONAL
14D6645X-RAY DIFFRACTION6.185TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2532-2.27880.35461680.32763439360788
2.2788-2.30570.28821920.28938704062100
2.3057-2.33380.28992030.273639514154100
2.3338-2.36330.32952150.273637994014100
2.3633-2.39440.2912170.272539034120100
2.3944-2.42720.31632160.280338334049100
2.4272-2.46190.32151930.271639264119100
2.4619-2.49860.31181920.267338404032100
2.4986-2.53770.31031630.247939414104100
2.5377-2.57930.25311810.243639054086100
2.5793-2.62380.26171710.23738984069100
2.6238-2.67150.28321980.231138624060100
2.6715-2.72290.25152070.230138744081100
2.7229-2.77850.26992170.219938714088100
2.7785-2.83890.24312230.211338594082100
2.8389-2.90490.23792310.212938144045100
2.9049-2.97760.24752260.20463842406899
2.9776-3.05810.22332440.19433845408999
3.0581-3.14810.26291940.18933794398899
3.1481-3.24970.22421680.17823883405198
3.2497-3.36580.21691970.17583820401799
3.3658-3.50060.22681940.16413820401498
3.5006-3.65990.23192140.1613783399798
3.6599-3.85290.16651570.1473792394997
3.8529-4.09430.16551880.15663760394896
4.0943-4.41040.17852070.13963737394496
4.4104-4.85430.18752140.14263695390997
4.8543-5.55660.17982080.14963820402898
5.5566-7.00040.1771990.15423798399798
7.0004-95.34020.19262240.14443761398598
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)
11.65280.2385-0.85792.1278-0.47242.44580.0206-0.4046-0.08280.5414-0.0674-0.0625-0.05010.1694-0.0210.32-0.0318-0.01910.26880.00560.201312.27135.861257.7699
22.5391-0.74690.98911.4987-0.75623.0953-0.0324-0.17160.36940.29680.0066-0.2109-0.54950.29720.01570.3751-0.1147-0.00740.2923-0.06580.318422.674654.476550.9862
31.29070.1071-0.14291.0965-0.15393.25090.0585-0.1728-0.05410.1322-0.006-0.23130.10430.332-0.03530.2429-0.0168-0.04240.2977-0.0240.291128.715235.308146.1206
42.9782-0.7117-0.89240.94350.98742.92130.0039-0.1342-0.0440.1617-0.0890.3086-0.0505-0.21450.06470.2757-0.03330.02510.1866-0.01250.2869-10.411146.33644.3898
51.9155-0.6584-0.43353.06840.99483.4619-0.10840.0696-0.26230.18880.01640.3770.5407-0.29750.05150.2913-0.0721-0.00340.22860.00330.2928-16.435634.072530.969
63.15740.0849-1.05791.39430.33312.15690.06650.12220.2033-0.1288-0.01470.2051-0.0788-0.2619-0.05150.24510.0076-0.02050.22560.04170.2549-9.137648.602622.0473
71.8-0.0843-0.26981.7865-0.07621.49920.03830.3375-0.1062-0.2332-0.0525-0.06680.1183-0.00250.00560.30950.0050.01990.3377-0.0240.247925.912924.847310.7554
81.0901-0.2261-0.77841.27380.01281.8526-0.0441-0.0114-0.09870.0420.0196-0.12040.1840.16460.03330.30070.0186-0.02640.2465-0.00050.239127.095422.117126.1169
91.7242-0.777-0.24691.88240.16022.01720.2670.71780.503-0.7713-0.2481-0.4346-0.36750.02860.15140.67680.0750.19490.46590.17960.380216.210253.76340.4397
102.5401-0.17370.37321.5548-0.03052.17980.0270.30060.833-0.105-0.0049-0.6688-0.33450.54930.05550.5039-0.06680.10360.49890.10810.646722.585667.555716.5554
110.99950.3856-0.40891.893-0.67573.00520.08210.24730.331-0.3784-0.0975-0.0409-0.2351-0.00520.00670.39550.00880.04920.25630.08310.35213.35261.511414.2492
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 118 )A0 - 118
2X-RAY DIFFRACTION2chain 'A' and (resid 119 through 239 )A119 - 239
3X-RAY DIFFRACTION3chain 'A' and (resid 240 through 362 )A240 - 362
4X-RAY DIFFRACTION4chain 'B' and (resid 0 through 92 )B0 - 92
5X-RAY DIFFRACTION5chain 'B' and (resid 93 through 266 )B93 - 266
6X-RAY DIFFRACTION6chain 'B' and (resid 267 through 362 )B267 - 362
7X-RAY DIFFRACTION7chain 'C' and (resid 0 through 216 )C0 - 216
8X-RAY DIFFRACTION8chain 'C' and (resid 217 through 362 )C217 - 362
9X-RAY DIFFRACTION9chain 'D' and (resid 0 through 110 )D0 - 110
10X-RAY DIFFRACTION10chain 'D' and (resid 111 through 239 )D111 - 239
11X-RAY DIFFRACTION11chain 'D' and (resid 240 through 362 )D240 - 362

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