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- PDB-4yji: The Crystal Structure of a Bacterial Aryl Acylamidase Belonging t... -

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Basic information

Entry
Database: PDB / ID: 4yji
TitleThe Crystal Structure of a Bacterial Aryl Acylamidase Belonging to the Amidase signature (AS) enzymes family
ComponentsAryl acylamidase
KeywordsHYDROLASE / amidase
Function / homology
Function and homology information


aryl-acylamidase / aryl-acylamidase activity
Similarity search - Function
Amidase / Amidase, conserved site / Amidases signature. / Amidase signature (AS) enzymes / Amidase signature (AS) domain / Amidase signature domain / Amidase signature (AS) superfamily / Amidase / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
N-(4-HYDROXYPHENYL)ACETAMIDE (TYLENOL) / Aryl acylamidase
Similarity search - Component
Biological speciesbacterium CSBL00001 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsChoi, I.-G. / Lee, S. / Park, E.-H. / Ko, H.-J. / Bang, W.-G.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2015
Title: Crystal structure analysis of a bacterial aryl acylamidase belonging to the amidase signature enzyme family
Authors: Lee, S. / Park, E.-H. / Ko, H.-J. / Bang, W.-G. / Kim, H.Y. / Kim, K.H. / Choi, I.-G.
History
DepositionMar 3, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aryl acylamidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6353
Polymers53,2631
Non-polymers3722
Water9,818545
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area440 Å2
ΔGint2 kcal/mol
Surface area18080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.980, 75.980, 214.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-683-

HOH

21A-700-

HOH

31A-718-

HOH

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Components

#1: Protein Aryl acylamidase


Mass: 53262.500 Da / Num. of mol.: 1 / Mutation: S187A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) bacterium CSBL00001 (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: C3UWD1, aryl-acylamidase
#2: Chemical ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID


Mass: 221.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM
#3: Chemical ChemComp-TYL / N-(4-HYDROXYPHENYL)ACETAMIDE (TYLENOL)


Mass: 151.163 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H9NO2 / Comment: medication*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 545 / 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: 2.91 Å3/Da / Density % sol: 57.72 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop
Details: 1.2 M NaH2PO4/0.8 M K2HPO4, 0.1 M CAPS pH 10.5, 0.2 M Li2SO4 and 0.1 M ZnCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.73→43.84 Å / Num. obs: 65840 / % possible obs: 98.6 % / Redundancy: 26.9 % / Net I/σ(I): 11.5

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
MOSFLMdata reduction
MOSFLMdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YJ6

4yj6


Resolution: 1.73→42.97 Å / SU ML: 0.14 / Cross valid method: NONE / σ(F): 0 / Phase error: 17.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.188 1937 3.04 %
Rwork0.1665 --
obs0.1672 63668 95.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.73→42.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3707 0 25 545 4277
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073819
X-RAY DIFFRACTIONf_angle_d1.085194
X-RAY DIFFRACTIONf_dihedral_angle_d12.5491395
X-RAY DIFFRACTIONf_chiral_restr0.043571
X-RAY DIFFRACTIONf_plane_restr0.006684
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.727-1.77020.26041230.26583956X-RAY DIFFRACTION87
1.7702-1.8180.28941250.23854026X-RAY DIFFRACTION89
1.818-1.87150.23681270.21644079X-RAY DIFFRACTION90
1.8715-1.9320.23291310.19674207X-RAY DIFFRACTION92
1.932-2.0010.21491410.17354374X-RAY DIFFRACTION95
2.001-2.08110.19051380.1634358X-RAY DIFFRACTION96
2.0811-2.17580.1741380.15564442X-RAY DIFFRACTION96
2.1758-2.29050.17891410.14864413X-RAY DIFFRACTION96
2.2905-2.4340.15481390.14864483X-RAY DIFFRACTION97
2.434-2.62190.17361400.16174536X-RAY DIFFRACTION98
2.6219-2.88570.18911450.16484554X-RAY DIFFRACTION98
2.8857-3.30320.18261460.16424658X-RAY DIFFRACTION99
3.3032-4.16110.17361470.154692X-RAY DIFFRACTION99
4.1611-42.98010.18241560.16424953X-RAY DIFFRACTION99

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