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- PDB-3g9u: Crystal structure of EstE5, was soaked by p-nitrophenyl butyrate ... -

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Basic information

Entry
Database: PDB / ID: 3g9u
TitleCrystal structure of EstE5, was soaked by p-nitrophenyl butyrate for 5min
ComponentsEsterase/lipase
KeywordsHYDROLASE / HSL / EstE5 / esterase / lipase
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
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.137, 61.137, 149.796
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 / Water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.02 Å3/Da / Density % sol: 39.11 %
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 295K
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: 2.2→20 Å / Num. obs: 14919 / % possible obs: 98.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Num. measured all: 87857
Reflection shellResolution: 2.2→2.28 Å / % possible all: 97.9

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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: 2.2→19.84 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.902 / SU B: 12.952 / SU ML: 0.15 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.274 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25106 751 5 %RANDOM
Rwork0.17883 ---
all0.18233 14919 --
obs0.18233 14162 98.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.196 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20 Å20 Å2
2--0.36 Å20 Å2
3----0.73 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2221 0 0 76 2297
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0222274
X-RAY DIFFRACTIONr_angle_refined_deg1.9241.9653085
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.945292
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.7532490
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.00415373
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.0851513
X-RAY DIFFRACTIONr_chiral_restr0.1540.2338
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021720
X-RAY DIFFRACTIONr_nbd_refined0.2180.21114
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21528
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2116
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2090.25
X-RAY DIFFRACTIONr_mcbond_it1.0731.51518
X-RAY DIFFRACTIONr_mcangle_it1.56522333
X-RAY DIFFRACTIONr_scbond_it2.7043893
X-RAY DIFFRACTIONr_scangle_it3.8694.5752
LS refinement shellResolution: 2.199→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 57 -
Rwork0.181 1001 -
obs--97.87 %
Refinement TLS params.Method: refined / Origin x: -15.1933 Å / Origin y: -18.4325 Å / Origin z: 37.514 Å
111213212223313233
T-0.0425 Å20.0277 Å2-0.0098 Å2--0.0428 Å2-0.0069 Å2---0.0285 Å2
L0.7322 °2-0.1497 °20.034 °2-0.7581 °2-0.2932 °2--0.9417 °2
S0.0356 Å °-0.01 Å °-0.0374 Å °-0.0418 Å °0.0174 Å °0.0814 Å °0.0085 Å °-0.0189 Å °-0.053 Å °

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