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- PDB-3g9t: Crystal structure of EstE5, was soaked by p-nitrophenyl butyrate ... -

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Basic information

Entry
Database: PDB / ID: 3g9t
TitleCrystal structure of EstE5, was soaked by p-nitrophenyl butyrate for 5sec
ComponentsEsterase/lipase
KeywordsHYDROLASE / HSL / EstE5 / esterase / lipase
Function / homology
Function and homology information


Lipase, GDXG, putative histidine active site / Lipase, GDXG, putative serine active site / Lipolytic enzymes "G-D-X-G" family, putative histidine active site. / Lipolytic enzymes "G-D-X-G" family, putative serine active site. / : / Alpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold ...Lipase, GDXG, putative histidine active site / Lipase, GDXG, putative serine active site / Lipolytic enzymes "G-D-X-G" family, putative histidine active site. / Lipolytic enzymes "G-D-X-G" family, putative serine 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
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsHwang, K.Y. / Nam, K.H.
CitationJournal: to be published
Title: Structural and biological characterization of EstE5
Authors: Hwang, K.Y. / Nam, K.H.
History
DepositionFeb 14, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / 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
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: Esterase/lipase


Theoretical massNumber of molelcules
Total (without water)34,6481
Polymers34,6481
Non-polymers00
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.245, 61.245, 148.418
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)
Gene: estE5 / Plasmid: pET / Production host: Escherichia coli (E. coli)
References: UniProt: Q0GMU2, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.01 Å3/Da / Density % sol: 38.76 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Tris-HCl pH 7.0-7.5, 2.2M ammonium sulfate, 0.2M lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K
PH range: 7.0-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 18, 2008
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.96→50 Å / Num. obs: 20799 / % possible obs: 98.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Num. measured all: 125727
Reflection shellResolution: 1.96→2.03 Å / % possible all: 97.4

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Processing

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

3fak


Resolution: 1.96→32.59 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.939 / SU B: 8.215 / SU ML: 0.108 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.183 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23022 1065 5.1 %RANDOM
Rwork0.19326 ---
all0.1951 20799 --
obs0.1951 19708 98.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.332 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å20 Å2
2--0.3 Å20 Å2
3----0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.96→32.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2221 0 0 99 2320
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222274
X-RAY DIFFRACTIONr_angle_refined_deg1.6851.9653085
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4815292
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.5392490
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.3715373
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.7411513
X-RAY DIFFRACTIONr_chiral_restr0.1320.2338
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021720
X-RAY DIFFRACTIONr_nbd_refined0.220.21155
X-RAY DIFFRACTIONr_nbtor_refined0.3110.21537
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2129
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1650.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0860.24
X-RAY DIFFRACTIONr_mcbond_it0.9941.51508
X-RAY DIFFRACTIONr_mcangle_it1.37922333
X-RAY DIFFRACTIONr_scbond_it2.423882
X-RAY DIFFRACTIONr_scangle_it3.4714.5752
LS refinement shellResolution: 1.96→2.01 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 84 -
Rwork0.205 1381 -
obs--97.21 %
Refinement TLS params.Method: refined / Origin x: -15.2454 Å / Origin y: -18.184 Å / Origin z: 37.1216 Å
111213212223313233
T-0.0748 Å20.0253 Å2-0.0077 Å2--0.0595 Å2-0.0044 Å2---0.0555 Å2
L1.4294 °2-0.8986 °20.0901 °2-1.3133 °2-0.6138 °2--1.683 °2
S0.0541 Å °0.0417 Å °-0.1165 Å °-0.051 Å °0.0241 Å °0.1401 Å °0.0575 Å °-0.1219 Å °-0.0781 Å °

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