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- PDB-3h18: Crystal structure of EstE5-PMSF (II) -

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Basic information

Entry
Database: PDB / ID: 3h18
TitleCrystal structure of EstE5-PMSF (II)
ComponentsEsterase/lipase
KeywordsHYDROLASE / HSL / EstE5 / esterase / lipase / PMSF / Phenylmethylsulfonyl fluoride
Function / homology
Function and homology information


Lipase, GDXG, putative serine active site / Lipolytic enzymes "G-D-X-G" family, putative serine active site. / Lipase, GDXG, putative histidine active site / Lipolytic enzymes "G-D-X-G" family, putative histidine active site. / Alpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
phenylmethanesulfonic acid / Esterase/lipase
Similarity search - Component
Biological speciesUncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHwang, K.Y. / Nam, K.H.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2009
Title: The crystal structure of an HSL-homolog EstE5 complex with PMSF reveals a unique configuration that inhibits the nucleophile Ser144 in catalytic triads.
Authors: Nam, K.H. / Kim, S.J. / Priyadarshi, A. / Kim, H.S. / Hwang, K.Y.
History
DepositionApr 11, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / 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_conn / 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_conn.pdbx_leaving_atom_flag / _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: Esterase/lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9923
Polymers34,6481
Non-polymers3442
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.283, 61.283, 149.894
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Esterase/lipase / EstE5


Mass: 34647.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Uncultured bacterium (environmental samples)
Description: soil Metagenome Library / Gene: estE5 / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q0GMU2, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases
#2: Chemical ChemComp-PMS / phenylmethanesulfonic acid


Mass: 172.202 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8O3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.03 Å3/Da / Density % sol: 39.44 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Tris-HCl pH 7.5, 2.2M ammonium sulfate, 0.2M lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1.23 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 20, 2009
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 10880 / % possible obs: 91.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Num. measured all: 60575
Reflection shellResolution: 2.4→2.49 Å / % possible all: 57.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
CNSrefinement
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FAK

3fak


Resolution: 2.4→28.36 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.904 / SU B: 21.438 / SU ML: 0.218 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.602 / ESU R Free: 0.304 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25986 529 4.9 %RANDOM
Rwork0.18422 ---
all0.18776 10880 --
obs0.18422 10338 91.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.984 Å2
Baniso -1Baniso -2Baniso -3
1-0.92 Å20 Å20 Å2
2--0.92 Å20 Å2
3----1.84 Å2
Refinement stepCycle: LAST / Resolution: 2.4→28.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2214 0 20 17 2251
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0222287
X-RAY DIFFRACTIONr_angle_refined_deg2.6141.9753100
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7245291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.4812490
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.59215373
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6321513
X-RAY DIFFRACTIONr_chiral_restr0.180.2339
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021734
X-RAY DIFFRACTIONr_nbd_refined0.2420.21078
X-RAY DIFFRACTIONr_nbtor_refined0.3190.21514
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2570.276
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.217
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.020.22
X-RAY DIFFRACTIONr_mcbond_it1.2661.51516
X-RAY DIFFRACTIONr_mcangle_it1.92522333
X-RAY DIFFRACTIONr_scbond_it3.2443913
X-RAY DIFFRACTIONr_scangle_it4.6384.5767
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 19 -
Rwork0.24 455 -
obs--55.9 %
Refinement TLS params.Method: refined / Origin x: -12.2459 Å / Origin y: 15.3867 Å / Origin z: -0.0073 Å
111213212223313233
T-0.0781 Å2-0.0121 Å2-0.0071 Å2--0.0592 Å20.0158 Å2---0.0735 Å2
L0.9738 °20.6101 °20.2257 °2-1.3156 °2-0.294 °2--2.4345 °2
S0.0355 Å °0.0511 Å °-0.0091 Å °-0.1637 Å °0.0213 Å °-0.1101 Å °0.1667 Å °0.1233 Å °-0.0568 Å °

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