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- PDB-4rgy: Structural and functional analysis of a low-temperature-active al... -

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Basic information

Entry
Database: PDB / ID: 4rgy
TitleStructural and functional analysis of a low-temperature-active alkaline esterase from South China Sea marine sediment microbial metagenomic library
ComponentsEsterase
KeywordsHYDROLASE
Function / homology: / Esterase-like / Putative esterase / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Esterase
Function and homology information
Biological speciesuncultured bacterium FLS12 (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsLiu, Y.
CitationJournal: J Ind Microbiol Biotechnol / Year: 2015
Title: Structural and functional analysis of a low-temperature-active alkaline esterase from South China Sea marine sediment microbial metagenomic library.
Authors: Hu, Y. / Liu, Y. / Li, J. / Feng, Y. / Lu, N. / Zhu, B. / Xue, S.
History
DepositionOct 1, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Database references
Revision 1.2Oct 28, 2015Group: Database references
Revision 1.3Feb 28, 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

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Assembly

Deposited unit
A: Esterase
B: Esterase


Theoretical massNumber of molelcules
Total (without water)60,5462
Polymers60,5462
Non-polymers00
Water11,602644
1
A: Esterase
B: Esterase

A: Esterase
B: Esterase


Theoretical massNumber of molelcules
Total (without water)121,0934
Polymers121,0934
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_757-x+2,y,-z+21
Buried area8440 Å2
ΔGint-22 kcal/mol
Surface area31290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.459, 63.767, 88.688
Angle α, β, γ (deg.)90.00, 127.11, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-319-

HOH

21B-303-

HOH

31B-312-

HOH

41B-330-

HOH

51B-335-

HOH

61B-352-

HOH

71B-581-

HOH

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Components

#1: Protein Esterase


Mass: 30273.170 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium FLS12 (environmental samples)
Production host: Escherichia coli (E. coli) / References: UniProt: B8Y562
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 644 / 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: 2.49 Å3/Da / Density % sol: 50.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.3 M Magnesium chloride hexahydrate, 0.1 M Tris hydrochloride, pH 8.5, 24% w/v PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.0001 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0001 Å / Relative weight: 1
ReflectionResolution: 1.4→35.067 Å / Num. obs: 101251 / % possible obs: 97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.4-1.72198.2
1.72-2.02198.5
2.02-2.8198.6
2.8-4.04196.8
4.04-50191.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→32.083 Å / SU ML: 0.09 / σ(F): 1.35 / Phase error: 20.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1813 5070 5.01 %RANDOM
Rwork0.1756 ---
all0.1813 95656 --
obs0.1759 95656 86.3 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→32.083 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3758 0 0 644 4402
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073863
X-RAY DIFFRACTIONf_angle_d1.1915243
X-RAY DIFFRACTIONf_dihedral_angle_d14.1891360
X-RAY DIFFRACTIONf_chiral_restr0.079558
X-RAY DIFFRACTIONf_plane_restr0.005679
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.41360.2384900.18721503X-RAY DIFFRACTION41
1.4136-1.43020.2314930.17842017X-RAY DIFFRACTION54
1.4302-1.44770.215870.17972120X-RAY DIFFRACTION57
1.4477-1.4660.18131140.17932203X-RAY DIFFRACTION60
1.466-1.48530.17591140.17722390X-RAY DIFFRACTION64
1.4853-1.50560.17391270.18842455X-RAY DIFFRACTION67
1.5056-1.52710.2021120.18632576X-RAY DIFFRACTION69
1.5271-1.54990.21081350.17822720X-RAY DIFFRACTION73
1.5499-1.57410.19221230.18152820X-RAY DIFFRACTION75
1.5741-1.60.20591590.1812911X-RAY DIFFRACTION79
1.6-1.62750.18471490.18143044X-RAY DIFFRACTION82
1.6275-1.65710.20571890.18533154X-RAY DIFFRACTION86
1.6571-1.6890.1941900.18343390X-RAY DIFFRACTION91
1.689-1.72350.19641990.19113546X-RAY DIFFRACTION96
1.7235-1.7610.20581960.18473637X-RAY DIFFRACTION98
1.761-1.80190.18682130.18253650X-RAY DIFFRACTION100
1.8019-1.8470.20521850.1833721X-RAY DIFFRACTION100
1.847-1.89690.19292000.18253678X-RAY DIFFRACTION100
1.8969-1.95270.2052020.17853705X-RAY DIFFRACTION100
1.9527-2.01580.17651970.17413726X-RAY DIFFRACTION100
2.0158-2.08780.17272080.16983677X-RAY DIFFRACTION100
2.0878-2.17140.17992010.17383737X-RAY DIFFRACTION100
2.1714-2.27020.20161940.17263709X-RAY DIFFRACTION100
2.2702-2.38980.17782000.17893740X-RAY DIFFRACTION100
2.3898-2.53950.1821960.17933731X-RAY DIFFRACTION100
2.5395-2.73550.17281960.17963719X-RAY DIFFRACTION100
2.7355-3.01070.19582050.18373696X-RAY DIFFRACTION100
3.0107-3.4460.16241990.17193724X-RAY DIFFRACTION99
3.446-4.34030.14921880.15133771X-RAY DIFFRACTION100
4.3403-35.0780.18582090.18343711X-RAY DIFFRACTION97

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