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- PDB-4g8b: Crystal structures of N-acyl homoserine lactonase AidH S102G muta... -

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Basic information

Entry
Database: PDB / ID: 4g8b
TitleCrystal structures of N-acyl homoserine lactonase AidH S102G mutant complexed with N-hexanoyl homoserine lactone
ComponentsAlpha/beta hydrolase fold protein
KeywordsHYDROLASE / AHL-lactonase / alpha/beta-hydrolase fold / cap-domain / AHL
Function / homology
Function and homology information


hydrolase activity, acting on ester bonds
Similarity search - Function
: / 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-[(3S)-2-oxotetrahydrofuran-3-yl]hexanamide / Alpha/beta hydrolase fold protein
Similarity search - Component
Biological speciesOchrobactrum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.302 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)61,6454
Polymers61,2472
Non-polymers3982
Water16,466914
1
A: Alpha/beta hydrolase fold protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8232
Polymers30,6231
Non-polymers1991
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)30,8232
Polymers30,6231
Non-polymers1991
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.385, 130.075, 44.254
Angle α, β, γ (deg.)90.00, 110.68, 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: 30623.342 Da / Num. of mol.: 2 / Mutation: S102G
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-HL6 / N-[(3S)-2-oxotetrahydrofuran-3-yl]hexanamide / N-hexanoyl-L-homoserine lactone


Mass: 199.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 914 / 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: 1.86 Å3/Da / Density % sol: 33.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 30% PEG8000, 0.2M LiAc, 0.1M NaAc, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.89 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: 0.89 Å / Relative weight: 1
ReflectionResolution: 1.302→27.51 Å / Num. obs: 108060 / % possible obs: 50.5 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3
Reflection shellResolution: 1.302→1.33 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: 1.302→27.51 Å / Occupancy max: 1 / Occupancy min: 0.19 / FOM work R set: 0.9168 / SU ML: 0.11 / σ(F): 1.35 / Phase error: 14.97 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1586 5266 4.88 %RANDOM
Rwork0.1218 ---
all0.15 ---
obs0.1237 107811 98.71 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 97.939 Å2 / ksol: 0.398 e/Å3
Displacement parametersBiso max: 99.96 Å2 / Biso mean: 16.9074 Å2 / Biso min: 5.23 Å2
Baniso -1Baniso -2Baniso -3
1-2.3934 Å20 Å2-3.7543 Å2
2---0.9133 Å20 Å2
3----1.4801 Å2
Refinement stepCycle: LAST / Resolution: 1.302→27.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4207 0 28 914 5149
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054502
X-RAY DIFFRACTIONf_angle_d1.0786118
X-RAY DIFFRACTIONf_chiral_restr0.071639
X-RAY DIFFRACTIONf_plane_restr0.005827
X-RAY DIFFRACTIONf_dihedral_angle_d12.9251723
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 (%)
1.3015-1.3480.2234590.172596511011093
1.348-1.4020.19945070.14591037510882100
1.402-1.46580.17885470.12011034510892100
1.4658-1.54310.16285240.10761034610870100
1.5431-1.63970.1515280.09651038210910100
1.6397-1.76630.15475550.09841034810903100
1.7663-1.9440.14625580.10421031810876100
1.944-2.22520.14795250.11741040810933100
2.2252-2.80310.15965520.12591034810900100
2.8031-27.51970.15365110.1331100241053596

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