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

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Basic information

Entry
Database: PDB / ID: 6bum
TitleCrystal structures of cyanuric acid hydrolase from Moorella thermoacetica
ComponentsCyanuric acid amidohydrolase
KeywordsHYDROLASE
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: 1.51 Å
AuthorsShi, K. / Cho, S. / Seffernick, J.L. / Bera, A. / Wackett, L.P. / 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: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / 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

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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)156,36937
Polymers153,9394
Non-polymers2,43033
Water21,0241167
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18970 Å2
ΔGint27 kcal/mol
Surface area44160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.440, 88.690, 204.280
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 , 5 types, 1200 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.: 24 / Source method: obtained synthetically / Formula: C3H8O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1167 / 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: 2.4 Å3/Da / Density % sol: 48.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 20%PEG3350, 100mMCaCl2

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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: 1.51→44.35 Å / Num. obs: 221630 / % possible obs: 95.8 % / Redundancy: 3.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.037 / Rsym value: 0.037 / Net I/σ(I): 20.1
Reflection shellResolution: 1.51→1.54 Å / Redundancy: 2 % / Rmerge(I) obs: 0.625 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 8020 / CC1/2: 0.471 / % possible all: 70.2

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Processing

Software
NameVersionClassification
PHENIX(1.13rc2_2975: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NQ4

3nq4


Resolution: 1.51→29.993 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 13.91
RfactorNum. reflection% reflection
Rfree0.141 20791 5.05 %
Rwork0.1261 --
obs0.1269 411321 91.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.51→29.993 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10744 0 153 1167 12064
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411112
X-RAY DIFFRACTIONf_angle_d0.76414987
X-RAY DIFFRACTIONf_dihedral_angle_d19.5544137
X-RAY DIFFRACTIONf_chiral_restr0.0691754
X-RAY DIFFRACTIONf_plane_restr0.0041979
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5102-1.52730.29754680.29258135X-RAY DIFFRACTION58
1.5273-1.54530.2924650.26759114X-RAY DIFFRACTION64
1.5453-1.56410.26785200.25929668X-RAY DIFFRACTION68
1.5641-1.58390.26774820.244610536X-RAY DIFFRACTION73
1.5839-1.60480.25235800.238411280X-RAY DIFFRACTION80
1.6048-1.62680.23645900.227212040X-RAY DIFFRACTION84
1.6268-1.650.22996630.207912697X-RAY DIFFRACTION90
1.65-1.67460.21796610.186413106X-RAY DIFFRACTION92
1.6746-1.70080.20197350.167113400X-RAY DIFFRACTION94
1.7008-1.72870.18156430.153613850X-RAY DIFFRACTION97
1.7287-1.75850.16587230.146114002X-RAY DIFFRACTION98
1.7585-1.79050.15567700.13613937X-RAY DIFFRACTION99
1.7905-1.82490.15238290.132913927X-RAY DIFFRACTION99
1.8249-1.86210.14597270.134113952X-RAY DIFFRACTION98
1.8621-1.90260.14497750.131313876X-RAY DIFFRACTION98
1.9026-1.94690.14697730.124113625X-RAY DIFFRACTION96
1.9469-1.99550.12388080.114113580X-RAY DIFFRACTION96
1.9955-2.04950.12577400.1113939X-RAY DIFFRACTION98
2.0495-2.10980.137360.106313889X-RAY DIFFRACTION98
2.1098-2.17790.11976680.100214046X-RAY DIFFRACTION99
2.1779-2.25570.11687200.101413735X-RAY DIFFRACTION97
2.2557-2.34590.12546820.099513810X-RAY DIFFRACTION97
2.3459-2.45270.11827370.101413774X-RAY DIFFRACTION97
2.4527-2.58190.127610.107213979X-RAY DIFFRACTION99
2.5819-2.74360.12357770.107913889X-RAY DIFFRACTION98
2.7436-2.95520.14177420.117713779X-RAY DIFFRACTION97
2.9552-3.25230.13187970.120513710X-RAY DIFFRACTION97
3.2523-3.72220.12346640.116713878X-RAY DIFFRACTION98
3.7222-4.68670.12657600.114713563X-RAY DIFFRACTION96
4.6867-29.99910.15467950.146813814X-RAY DIFFRACTION98

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