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- PDB-4g5x: Crystal structures of N-acyl homoserine lactonase AidH -

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Basic information

Entry
Database: PDB / ID: 4g5x
TitleCrystal structures of N-acyl homoserine lactonase AidH
ComponentsAlpha/beta hydrolase fold proteinAlpha/beta hydrolase superfamily
KeywordsHYDROLASE / alpha/beta-hydrolase fold / core domain / eight-stranded sheet / lactonase
Function / homology
Function and homology information


hydrolase activity, acting on ester bonds
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
Alpha/beta hydrolase fold protein
Similarity search - Component
Biological speciesOchrobactrum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.29 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 18, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)61,3072
Polymers61,3072
Non-polymers00
Water16,268903
1
A: Alpha/beta hydrolase fold protein


Theoretical massNumber of molelcules
Total (without water)30,6531
Polymers30,6531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Alpha/beta hydrolase fold protein


Theoretical massNumber of molelcules
Total (without water)30,6531
Polymers30,6531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.414, 129.490, 44.759
Angle α, β, γ (deg.)90.00, 111.11, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Alpha/beta hydrolase fold protein / Alpha/beta hydrolase superfamily


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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 903 / 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: 1.87 Å3/Da / Density % sol: 34.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.29→20 Å / Num. obs: 124835 / % possible obs: 55.3 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Biso Wilson estimate: 11.42 Å2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.29→19.87 Å / Occupancy max: 1 / Occupancy min: 0.11 / FOM work R set: 0.9127 / SU ML: 0.15 / σ(F): 0 / Phase error: 15.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1579 4727 5.05 %RANDOM
Rwork0.1228 ---
all0.15 ---
obs0.1246 93530 83.01 %-
Solvent computationShrinkage radii: 0.49 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 102.138 Å2 / ksol: 0.458 e/Å3
Displacement parametersBiso max: 94.92 Å2 / Biso mean: 20.9681 Å2 / Biso min: 6.74 Å2
Baniso -1Baniso -2Baniso -3
1-1.2813 Å2-0 Å21.2702 Å2
2--0.5155 Å20 Å2
3----1.7968 Å2
Refinement stepCycle: LAST / Resolution: 1.29→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4216 0 0 903 5119
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064562
X-RAY DIFFRACTIONf_angle_d1.0646211
X-RAY DIFFRACTIONf_chiral_restr0.073648
X-RAY DIFFRACTIONf_plane_restr0.005845
X-RAY DIFFRACTIONf_dihedral_angle_d12.3861737
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 (%)
1.29-1.33610.2654400.21858073851376
1.3361-1.38960.24474190.18538144856377
1.3896-1.45280.21744250.14398309873477
1.4528-1.52940.17844730.11268468894180
1.5294-1.62520.15815000.10088521902180
1.6252-1.75060.14294190.09768614903380
1.7506-1.92660.14564840.1038596908081
1.9266-2.20510.14344890.1129429991888
2.2051-2.7770.15145560.1217102751083196
2.777-19.8720.14755220.1259103741089696

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