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- PDB-5t13: Structure of the Cyanuric Acid Hydrolase TrzD Reveals Product Exi... -

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Basic information

Entry
Database: PDB / ID: 5t13
TitleStructure of the Cyanuric Acid Hydrolase TrzD Reveals Product Exit Channel
ComponentsCyanuric acid amidohydrolase
KeywordsHYDROLASE / TrzD - cyanuric acid hydrolase from Acidovorax citrulli / AtzD - cyanuric acid hydrolase from Pseudomonas sp ADP / ACAH - cyanuric acid hydrolase from Azorhizobium calindulans.
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
CARBON DIOXIDE / Cyanuric acid amidohydrolase
Similarity search - Component
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsBera, A.K. / Wackett, L.P.
Funding support United States, 1items
OrganizationGrant numberCountry
MnDRIVE Transdisciplinary Research grant United States
CitationJournal: Sci Rep / Year: 2017
Title: Structure of the Cyanuric Acid Hydrolase TrzD Reveals Product Exit Channel.
Authors: Bera, A.K. / Aukema, K.G. / Elias, M. / Wackett, L.P.
History
DepositionAug 17, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyanuric acid amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4054
Polymers40,2921
Non-polymers1123
Water3,099172
1
A: Cyanuric acid amidohydrolase
hetero molecules

A: Cyanuric acid amidohydrolase
hetero molecules

A: Cyanuric acid amidohydrolase
hetero molecules

A: Cyanuric acid amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,61916
Polymers161,1694
Non-polymers44912
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area12250 Å2
ΔGint-70 kcal/mol
Surface area51030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.591, 90.686, 120.075
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-564-

HOH

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Components

#1: Protein Cyanuric acid amidohydrolase


Mass: 40292.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae (bacteria) / Gene: trzD / Production host: Escherichia coli (E. coli) / References: UniProt: P0A3V4, cyanuric acid amidohydrolase
#2: Chemical ChemComp-CO2 / CARBON DIOXIDE


Mass: 44.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.3 Å3/Da / Density % sol: 46.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 0.05 M Ammonium sulfate, 0.05 M BIS-TRIS pH 6.2, 30% Pentaerythritol ethoxylate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03322 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03322 Å / Relative weight: 1
ReflectionResolution: 2.14→29.45 Å / Num. obs: 19361 / % possible obs: 99.8 % / Redundancy: 5.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.2
Reflection shellResolution: 2.19→2.26 Å / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 2.6 / CC1/2: 0.76 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BVQ

4bvq


Resolution: 2.19→29.45 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2003 1825 5 %
Rwork0.1517 --
obs0.1542 36528 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.19→29.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2816 0 7 172 2995
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012875
X-RAY DIFFRACTIONf_angle_d1.0123891
X-RAY DIFFRACTIONf_dihedral_angle_d11.4241733
X-RAY DIFFRACTIONf_chiral_restr0.057445
X-RAY DIFFRACTIONf_plane_restr0.006519
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1896-2.24880.30691370.24312633X-RAY DIFFRACTION97
2.2488-2.3150.27431400.21712648X-RAY DIFFRACTION100
2.315-2.38970.22651400.19582716X-RAY DIFFRACTION100
2.3897-2.4750.2381410.18822647X-RAY DIFFRACTION99
2.475-2.57410.2341440.17862700X-RAY DIFFRACTION100
2.5741-2.69110.20541400.16442651X-RAY DIFFRACTION100
2.6911-2.83290.23651360.17232668X-RAY DIFFRACTION100
2.8329-3.01020.21181430.18012669X-RAY DIFFRACTION100
3.0102-3.24240.22861420.16012678X-RAY DIFFRACTION99
3.2424-3.56820.21951400.14522668X-RAY DIFFRACTION99
3.5682-4.08340.16421350.12342675X-RAY DIFFRACTION100
4.0834-5.14010.14771410.10612678X-RAY DIFFRACTION100
5.1401-29.45290.16321460.13522672X-RAY DIFFRACTION100

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