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- PDB-1tqh: Covalent Reaction intermediate Revealed in Crystal Structure of t... -

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Basic information

Entry
Database: PDB / ID: 1tqh
TitleCovalent Reaction intermediate Revealed in Crystal Structure of the Geobacillus stearothermophilus Carboxylesterase Est30
ComponentsCarboxylesterase precursor
KeywordsHYDROLASE / CARBOXYLESTERASE / TETRAHEDRAL INTERMEDIATE / ALPHA/BETA HYDROLASE
Function / homology
Function and homology information


carboxylesterase / lipase activity / carboxylesterase activity / membrane
Similarity search - Function
Esterase/lipase / Serine aminopeptidase, S33 / Serine aminopeptidase, S33 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PROPYL ACETATE / Carboxylesterase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.63 Å
AuthorsLiu, P. / Wang, Y.F. / Ewis, H.E. / Abdelal, A.T. / Lu, C.D. / Harrison, R.W. / Weber, I.T.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Covalent reaction intermediate revealed in crystal structure of the Geobacillus stearothermophilus carboxylesterase Est30.
Authors: Liu, P. / Wang, Y.F. / Ewis, H.E. / Abdelal, A.T. / Lu, C.D. / Harrison, R.W. / Weber, I.T.
History
DepositionJun 17, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 30, 2014Group: Data collection
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carboxylesterase precursor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7164
Polymers28,4211
Non-polymers2943
Water2,756153
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.654, 58.205, 179.045
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Carboxylesterase precursor


Mass: 28421.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: Q06174, carboxylesterase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-4PA / PROPYL ACETATE


Mass: 102.132 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: LITHIUM SULFATE, PEG400, DIOXANE, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1951
2951
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONAPS 22-ID10.99997
SYNCHROTRONAPS 22-ID20.97920, 0.97933, 0.971602, 0.987072
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDOct 22, 2003
MAR CCD 165 mm2CCDMar 6, 2003
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SISINGLE WAVELENGTHMx-ray1
2SIMADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.999971
20.97921
30.979331
40.9716021
50.9870721
ReflectionResolution: 1.63→50 Å / Num. obs: 36452 / % possible obs: 97.5 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.155
Reflection shellResolution: 1.63→1.69 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.181 / Mean I/σ(I) obs: 14.3 / Num. unique all: 35555 / % possible all: 90.5

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Processing

Software
NameClassification
HKL-2000data collection
HKL-2000data reduction
SOLVEphasing
RESOLVEmodel building
ARP/wARPmodel building
SHELXL-97refinement
MAR345data collection
HKL-2000data scaling
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.63→10 Å / Num. parameters: 19536 / Num. restraintsaints: 24598 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2279 1768 5 %RANDOM
Rwork0.1681 ---
all0.1714 35376 --
obs--96.7 %-
Refine analyzeNum. disordered residues: 9 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2115
Refinement stepCycle: LAST / Resolution: 1.63→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1959 0 17 153 2129
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.008
X-RAY DIFFRACTIONs_angle_d0.024
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0245
X-RAY DIFFRACTIONs_zero_chiral_vol0.038
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.051
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.011
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.002
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.038
X-RAY DIFFRACTIONs_approx_iso_adps0.087

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