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- PDB-4g9e: Crystal structures of N-acyl homoserine lactonase AidH complexed ... -

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Basic information

Entry
Database: PDB / ID: 4g9e
TitleCrystal structures of N-acyl homoserine lactonase AidH complexed with N-butanoyl homoserine
ComponentsAlpha/beta hydrolase fold protein
KeywordsHYDROLASE / alpha/beta-hydrolase fold / AHL-lactonase / AHL-binding
Function / homology
Function and homology information


hydrolase activity, acting on ester bonds / membrane
Similarity search - Function
: / Alpha/beta hydrolase family / Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N-butanoyl-L-homoserine / Alpha/beta hydrolase fold protein
Similarity search - Component
Biological speciesOchrobactrum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.088 Å
AuthorsLiang, D.C. / Yan, X.X. / Gao, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: High-resolution structures of AidH complexes provide insights into a novel catalytic mechanism for N-acyl homoserine lactonase
Authors: Gao, A. / Mei, G.Y. / Liu, S. / Wang, P. / Tang, Q. / Liu, Y.P. / Wen, H. / An, X.M. / Zhang, L.Q. / Yan, X.X. / Liang, D.C.
History
DepositionJul 23, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 16, 2013Provider: 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 / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Alpha/beta hydrolase fold protein
B: Alpha/beta hydrolase fold protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6854
Polymers61,3072
Non-polymers3782
Water16,880937
1
A: Alpha/beta hydrolase fold protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8432
Polymers30,6531
Non-polymers1891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Alpha/beta hydrolase fold protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8432
Polymers30,6531
Non-polymers1891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.164, 129.523, 44.312
Angle α, β, γ (deg.)90.00, 111.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Alpha/beta hydrolase fold protein / AHL-lactonase


Mass: 30653.365 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ochrobactrum (bacteria) / Strain: T63 / Gene: aidH / Production host: Escherichia coli (E. coli) / References: UniProt: D2J2T6
#2: Chemical ChemComp-C4L / N-butanoyl-L-homoserine


Mass: 189.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 937 / 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: 1.84 Å3/Da / Density % sol: 33.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% PEG8000, 0.2M ammonium acetate, 0.01M magnesium acetate, 0.05M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 22, 2011
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.088→21.29 Å / Num. obs: 179801 / % possible obs: 52.1 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Biso Wilson estimate: 7.83 Å2
Reflection shellResolution: 1.09→1.12 Å / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G5X

4g5x


Resolution: 1.088→21.29 Å / Occupancy max: 1 / Occupancy min: 0.07 / FOM work R set: 0.9246 / SU ML: 0.1 / σ(F): 1.34 / Phase error: 13.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1517 8930 4.97 %
Rwork0.1273 --
all0.15 --
obs0.1285 179678 97.33 %
Solvent computationShrinkage radii: 0.04 Å / VDW probe radii: 0.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 148.829 Å2 / ksol: 0.544 e/Å3
Displacement parametersBiso max: 57.21 Å2 / Biso mean: 15.5626 Å2 / Biso min: 4.1 Å2
Baniso -1Baniso -2Baniso -3
1-2.5727 Å2-0 Å20.012 Å2
2---2.7408 Å20 Å2
3----0.5636 Å2
Refinement stepCycle: LAST / Resolution: 1.088→21.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4216 0 26 937 5179
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054616
X-RAY DIFFRACTIONf_angle_d1.0496290
X-RAY DIFFRACTIONf_chiral_restr0.073657
X-RAY DIFFRACTIONf_plane_restr0.005849
X-RAY DIFFRACTIONf_dihedral_angle_d12.0311749
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.0884-1.12730.24238090.2232163171712693
1.1273-1.17250.18539030.1661169471785096
1.1725-1.22580.1629100.1339169901790097
1.2258-1.29040.14288550.1166171341798998
1.2904-1.37130.14749250.111171761810198
1.3713-1.47710.14099010.1058173131821499
1.4771-1.62570.12599390.1016173891832899
1.6257-1.86090.14489280.11141745718385100
1.8609-2.3440.14679020.1211174361833899
2.344-21.2940.15368580.1374165891744794

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