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- PDB-3a1i: Crystal structure of Rhodococcus sp. N-771 Amidase complexed with... -

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Basic information

Entry
Database: PDB / ID: 3a1i
TitleCrystal structure of Rhodococcus sp. N-771 Amidase complexed with Benzamide
ComponentsAmidase
KeywordsHYDROLASE / amidase / AS family enzyme
Function / homology
Function and homology information


Glu-tRNAGln amidotransferase C subunit, N-terminal domain / Amidase / Amidase, conserved site / Amidases signature. / Amidase signature (AS) enzymes / Amidase signature (AS) domain / Amidase signature domain / Amidase signature (AS) superfamily / Amidase / Histone, subunit A ...Glu-tRNAGln amidotransferase C subunit, N-terminal domain / Amidase / Amidase, conserved site / Amidases signature. / Amidase signature (AS) enzymes / Amidase signature (AS) domain / Amidase signature domain / Amidase signature (AS) superfamily / Amidase / Histone, subunit A / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesRhodococcus sp. N-771 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsOhtaki, A. / Noguchi, K. / Sato, Y. / Murata, K. / Odaka, M. / Yohda, M.
CitationJournal: Biochim.Biophys.Acta / Year: 2009
Title: Structure and Characterization of Amidase from Rhodococcus sp. N-771: Insight into the Molecular Mechanism of Substrate Recognition
Authors: Ohtaki, A. / Murata, K. / Sato, Y. / Noguchi, K. / Miyatake, H. / Dohmae, N. / Yamada, K. / Yohda, M. / Odaka, M.
History
DepositionApr 3, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8672
Polymers54,7461
Non-polymers1211
Water3,963220
1
A: Amidase
hetero molecules

A: Amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,7354
Polymers109,4932
Non-polymers2422
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area9270 Å2
ΔGint-67 kcal/mol
Surface area31740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.272, 92.272, 161.799
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-563-

HOH

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Components

#1: Protein Amidase


Mass: 54746.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus sp. N-771 (bacteria) / Gene: ami / Plasmid: pET23a / Production host: Escherichia coli (E. coli) / References: UniProt: Q7DKE4, amidase
#2: Chemical ChemComp-UNU / BENZAMIDE


Mass: 121.137 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H7NO
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 3.14 Å3/Da / Density % sol: 60.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 15% polyethylene glycol 4000, 100mM magnesium chloride, 100mM calcium chloride, 100mM Mes, pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 13, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.17→50 Å / Num. obs: 30854 / % possible obs: 99.5 %

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2G3I

2g3i


Resolution: 2.32→50 Å
RfactorNum. reflection% reflection
Rfree0.233 2915 -
Rwork0.199 --
obs-29155 94 %
Refinement stepCycle: LAST / Resolution: 2.32→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3758 0 9 220 3987

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