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- PDB-2uxy: Aliphatic amidase -

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Basic information

Entry
Database: PDB / ID: 2uxy
TitleAliphatic amidase
ComponentsALIPHATIC AMIDASE
KeywordsHYDROLASE / NITRILASE SUPERFAMILY / PSEUDOMONAS AERUGINOSA / ACYL TRANSFER / THIOL ENZYMES / HYDROXAMIC ACID / ALIPHATIC AMIDASE
Function / homology
Function and homology information


amidase / indoleacetamide hydrolase activity / amide catabolic process / carbon utilization / amidase activity / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
Similarity search - Function
Aliphatic amidase / Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.25 Å
AuthorsAndrade, J. / KArmali, A. / Carrondo, M.A. / Frazao, C.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Structure of Amidase from Pseudomonas Aeruginosa Showing a Trapped Acyl Transfer Reaction Intermediate State.
Authors: Andrade, J. / Karmali, A. / Carrondo, M.A. / Frazao, C.
History
DepositionApr 2, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ALIPHATIC AMIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1362
Polymers38,0401
Non-polymers961
Water5,495305
1
A: ALIPHATIC AMIDASE
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)228,81712
Polymers228,2416
Non-polymers5766
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/21
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation11_655-x+y+1,y,-z+1/21
MethodPQS
Unit cell
Length a, b, c (Å)102.706, 102.706, 151.320
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-2001-

HOH

21A-2108-

HOH

31A-2236-

HOH

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Components

#1: Protein ALIPHATIC AMIDASE / ACYLAMIDE AMIDOHYDROLASE


Mass: 38040.121 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-341 / Source method: isolated from a natural source
Details: AN ACYL REACTION INTERMEDIATE WAS FOUND BOUNT TO SG OF CYS166
Source: (natural) PSEUDOMONAS AERUGINOSA (bacteria) / References: UniProt: P11436, amidase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 305 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAN ACYL TRANSFER REACTION INERMEDIATE IS COVALENTLY BOUND TO SG ATOM OF CYS166

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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: 2.26 Å3/Da / Density % sol: 45.5 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 6.8
Details: VAPOUR DIFFUSION IN SITTING DROPS OF 5 MICRO-L OF 25 MG/ML PROTEIN SOLUTION IN 50 MM TRIS-HCL PH 7.2, 5 MM DTT AND 1 MM EDTA, PLUS 2 MICRO-L OF WELL SOLUTION 15% PEG 4K AND 0.2M AMMONIUM SULPHATE PH 6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9756
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 17, 2005 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9756 Å / Relative weight: 1
ReflectionResolution: 1.25→42.67 Å / Num. obs: 115216 / % possible obs: 89 % / Observed criterion σ(I): 0 / Redundancy: 13.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 24.9
Reflection shellResolution: 1.25→1.28 Å / Rmerge(I) obs: 0.5 / % possible all: 51.5

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Processing

Software
NameVersionClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXCDphasing
SHELXDphasing
SHELXEIN HKL2MAPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.25→1.28 Å / Num. parameters: 27871 / Num. restraintsaints: 35602 / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: ENGH AND HUBER DICTIONARY WAS SETUP ASSUMING A SP3 HYBRIDIZATION ON THE CENTRAL CARBON WITH A SINGLE BOND TO ITS NEIGHBORING OXYGEN
RfactorNum. reflection% reflectionSelection details
Rfree0.1355 1744 1.5 %RANDOM
all0.1107 115216 --
obs0.1112 -51.5 %-
Refine analyzeNum. disordered residues: 28 / Occupancy sum hydrogen: 2538.86 / Occupancy sum non hydrogen: 2968.5
Refinement stepCycle: LAST / Resolution: 1.25→1.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2661 0 5 305 2971
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0317
X-RAY DIFFRACTIONs_zero_chiral_vol0.08
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.083
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.131
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.043
X-RAY DIFFRACTIONs_approx_iso_adps0.099

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