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- PDB-4j7a: Crystal Structure of Est25 - a Bacterial Homolog of Hormone-Sensi... -

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Basic information

Entry
Database: PDB / ID: 4j7a
TitleCrystal Structure of Est25 - a Bacterial Homolog of Hormone-Sensitive Lipase from a Metagenomic Library
ComponentsEsterase
KeywordsHYDROLASE / alpha/beta
Function / homologyAlpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / hydrolase activity / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Esterase
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.492 Å
AuthorsNgo, T.D. / Ryu, B.H. / Ju, H.S. / Jang, E.J. / Park, K.S. / Joo, S.B. / Kim, K.K. / Kim, D.H.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structural and functional analyses of a bacterial homologue of hormone-sensitive lipase from a metagenomic library
Authors: Ngo, T.D. / Ryu, B.H. / Ju, H. / Jang, E. / Park, K. / Kim, K.K. / Kim, D.H.
History
DepositionFeb 13, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: Esterase
B: Esterase
C: Esterase
D: Esterase


Theoretical massNumber of molelcules
Total (without water)158,9784
Polymers158,9784
Non-polymers00
Water38,0302111
1
A: Esterase
D: Esterase


Theoretical massNumber of molelcules
Total (without water)79,4892
Polymers79,4892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-8 kcal/mol
Surface area24140 Å2
MethodPISA
2
B: Esterase
C: Esterase


Theoretical massNumber of molelcules
Total (without water)79,4892
Polymers79,4892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-9 kcal/mol
Surface area24180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)197.758, 95.213, 99.418
Angle α, β, γ (deg.)90.00, 97.05, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-674-

HOH

21B-697-

HOH

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Components

#1: Protein
Esterase /


Mass: 39744.430 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: UniProt: Q4TZQ3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2111 / 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: 2.92 Å3/Da / Density % sol: 57.9 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 7
Details: 2.4M sodium malonate pH 7.0, Microbatch, temperature 295K

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Data collection

DiffractionMean temperature: 203 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.97888, 0.97917, 0.96395, 1.00000
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationMonochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978881
20.979171
30.963951
411
ReflectionResolution: 1.49→50 Å / Num. all: 297211 / Num. obs: 285917 / % possible obs: 96.2 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3
Reflection shellResolution: 1.49→50 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 3.6 / % possible all: 96.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine: 1.8_1063)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.492→28.555 Å / SU ML: 0.11 / σ(F): 1.34 / Phase error: 14.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1695 14491 5.07 %RANDOM
Rwork0.1434 ---
all0.15 297185 --
obs0.1448 285892 96.51 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.492→28.555 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10560 0 0 2111 12671
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610812
X-RAY DIFFRACTIONf_angle_d1.17714760
X-RAY DIFFRACTIONf_dihedral_angle_d12.7013860
X-RAY DIFFRACTIONf_chiral_restr0.0781652
X-RAY DIFFRACTIONf_plane_restr0.0061956
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.492-1.5090.22234030.1711846390
1.509-1.52680.22284790.164885495
1.5268-1.54540.20335000.1447883695
1.5454-1.56490.17914670.1389894596
1.5649-1.58550.16775090.1288881295
1.5855-1.60730.16054570.125896596
1.6073-1.63020.16425030.1255893196
1.6302-1.65450.17224980.127898196
1.6545-1.68040.16555030.1256897996
1.6804-1.70790.1634530.1238905596
1.7079-1.73740.16114860.1249902996
1.7374-1.7690.17744950.1368906897
1.769-1.8030.19554770.136903597
1.803-1.83980.15975020.1288908597
1.8398-1.87980.16085130.1268905997
1.8798-1.92350.175100.1324909797
1.9235-1.97160.16914650.1343913198
1.9716-2.02490.16934960.1362919698
2.0249-2.08450.16064520.1299919798
2.0845-2.15170.15384630.1273922498
2.1517-2.22860.16464800.1307920698
2.2286-2.31780.16345040.134925199
2.3178-2.42320.15825060.1375928299
2.4232-2.55090.18785170.1467930899
2.5509-2.71060.18224710.1507930699
2.7106-2.91970.16454520.1561939899
2.9197-3.21320.17944710.1554936499
3.2132-3.67730.14785040.1383922398
3.6773-4.62980.14944730.1429874693
4.6298-28.560.20194820.1861837588

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