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- PDB-4ob8: Crystal structure of a novel thermostable esterase from Pseudomon... -

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Basic information

Entry
Database: PDB / ID: 4ob8
TitleCrystal structure of a novel thermostable esterase from Pseudomonas putida ECU1011
ComponentsAlpha/beta hydrolase fold-3 domain protein
KeywordsHYDROLASE / A/B HYDROLASE FOLD / Esterase / HSL-like family
Function / homology
Function and homology information


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
DI(HYDROXYETHYL)ETHER / Alpha/beta hydrolase fold-3 domain protein
Similarity search - Component
Biological speciesPseudomonas (RNA similarity group I)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.801 Å
AuthorsDou, S. / Kong, X.D. / Ma, B.D. / Xu, J.H. / Zhou, J.H.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2014
Title: Crystal structures of Pseudomonas putida esterase reveal the functional role of residues 187 and 287 in substrate binding and chiral recognition
Authors: Dou, S. / Kong, X.D. / Ma, B.D. / Chen, Q. / Zhang, J. / Zhou, J.H. / Xu, J.H.
History
DepositionJan 7, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Nov 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-3 domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1023
Polymers36,8781
Non-polymers2242
Water6,575365
1
A: Alpha/beta hydrolase fold-3 domain protein
hetero molecules

A: Alpha/beta hydrolase fold-3 domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,2046
Polymers73,7552
Non-polymers4494
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)95.633, 95.633, 87.806
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-572-

HOH

21A-604-

HOH

31A-622-

HOH

41A-647-

HOH

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Components

#1: Protein Alpha/beta hydrolase fold-3 domain protein


Mass: 36877.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas (RNA similarity group I) / Strain: ECU1011 / Plasmid: pET21A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: L7PYQ2, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 365 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHOR STATED THE SEQUENCE DATABASE WAS WRONG AT THIS POSITION.

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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: 2.72 Å3/Da / Density % sol: 54.81 % / Mosaicity: 0.785 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Hepes/Mops-Na, pH 7.5, 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.03M MgCl2, 0.03M CaCl2, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 17, 2013
RadiationMonochromator: VARIMAX-HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→42.8 Å / Num. obs: 38145 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 25.5 % / Biso Wilson estimate: 24.75 Å2 / Rmerge(I) obs: 0.092 / Χ2: 1.05 / Net I/σ(I): 19
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.8-1.8625.60.4137321.081100
1.86-1.9425.80.32237621.0511100
1.94-2.0325.90.26137731.049199.9
2.03-2.1325.70.21237571.099199.9
2.13-2.2725.40.17537971.042199.8
2.27-2.4425.50.14138051.031199.9
2.44-2.6925.80.11237951.052199.8
2.69-3.0825.80.08538461.061199.7
3.08-3.8825.40.06538501.007199.1
3.88-5024.60.06740281.029198

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YH2

2yh2


Resolution: 1.801→42.768 Å / Occupancy max: 1 / Occupancy min: 0.46 / FOM work R set: 0.9031 / SU ML: 0.13 / σ(F): 1.34 / Phase error: 15.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1823 1907 5.01 %
Rwork0.1489 --
obs0.1505 38081 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.64 Å2 / Biso mean: 25.2135 Å2 / Biso min: 12.42 Å2
Refinement stepCycle: LAST / Resolution: 1.801→42.768 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2427 0 15 365 2807
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062523
X-RAY DIFFRACTIONf_angle_d1.0743431
X-RAY DIFFRACTIONf_chiral_restr0.073381
X-RAY DIFFRACTIONf_plane_restr0.005448
X-RAY DIFFRACTIONf_dihedral_angle_d13.629921
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8011-1.84610.18681240.144725442668100
1.8461-1.8960.17821410.137925442685100
1.896-1.95180.17421360.14625462682100
1.9518-2.01480.19421330.14425592692100
2.0148-2.08680.16391240.137525682692100
2.0868-2.17040.16471170.144225682685100
2.1704-2.26920.19471450.141925602705100
2.2692-2.38880.15521640.148525402704100
2.3888-2.53840.17711370.155225832720100
2.5384-2.73440.20361370.155425922729100
2.7344-3.00950.17831430.154525842727100
3.0095-3.44480.18071410.15182599274099
3.4448-4.33950.19241220.14112637275998
4.3395-42.78040.18481430.15552750289398

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