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- PDB-8ilt: Crystal structure of Est30 -

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Basic information

Entry
Database: PDB / ID: 8ilt
TitleCrystal structure of Est30
ComponentsCarboxylesterase
KeywordsHYDROLASE / Carboxylesterase / enzyme
Function / homologyEsterase/lipase / : / Serine aminopeptidase, S33 / carboxylesterase / Serine aminopeptidase, S33 / carboxylesterase activity / Alpha/Beta hydrolase fold / Carboxylesterase
Function and homology information
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsFeng, Y. / Luo, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)32000901 China
CitationJournal: To Be Published
Title: Crystal structure of Est30
Authors: Feng, Y. / Luo, Z.
History
DepositionMar 4, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carboxylesterase
B: Carboxylesterase
C: Carboxylesterase
D: Carboxylesterase
E: Carboxylesterase
F: Carboxylesterase
G: Carboxylesterase
H: Carboxylesterase
I: Carboxylesterase


Theoretical massNumber of molelcules
Total (without water)265,6869
Polymers265,6869
Non-polymers00
Water7,476415
1
A: Carboxylesterase


Theoretical massNumber of molelcules
Total (without water)29,5211
Polymers29,5211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Carboxylesterase


Theoretical massNumber of molelcules
Total (without water)29,5211
Polymers29,5211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Carboxylesterase


Theoretical massNumber of molelcules
Total (without water)29,5211
Polymers29,5211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Carboxylesterase


Theoretical massNumber of molelcules
Total (without water)29,5211
Polymers29,5211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Carboxylesterase


Theoretical massNumber of molelcules
Total (without water)29,5211
Polymers29,5211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Carboxylesterase


Theoretical massNumber of molelcules
Total (without water)29,5211
Polymers29,5211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Carboxylesterase


Theoretical massNumber of molelcules
Total (without water)29,5211
Polymers29,5211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Carboxylesterase


Theoretical massNumber of molelcules
Total (without water)29,5211
Polymers29,5211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Carboxylesterase


Theoretical massNumber of molelcules
Total (without water)29,5211
Polymers29,5211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)149.964, 59.988, 166.039
Angle α, β, γ (deg.)90.00, 99.24, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Carboxylesterase / Est30


Mass: 29520.619 Da / Num. of mol.: 9 / Mutation: M126S, G129L, I170K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: est, est30 / Production host: Escherichia coli (E. coli) / References: UniProt: Q06174, carboxylesterase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 415 / 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: 2.84 Å3/Da / Density % sol: 56.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: Zinc acetate tetrahydrate, PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.42→49.54 Å / Num. obs: 112238 / % possible obs: 100 % / Redundancy: 6.73 % / CC1/2: 0.99 / Net I/σ(I): 10.78
Reflection shellResolution: 2.42→2.48 Å / Num. unique obs: 8256 / CC1/2: 0.6998

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
XDSdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.42→49.54 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.908 / SU B: 14.079 / SU ML: 0.29 / Cross valid method: THROUGHOUT / ESU R: 0.404 / ESU R Free: 0.282 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27318 5611 5 %RANDOM
Rwork0.21406 ---
obs0.21699 106615 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.686 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20 Å2-1.11 Å2
2--4.36 Å2-0 Å2
3----4.2 Å2
Refinement stepCycle: 1 / Resolution: 2.42→49.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18229 0 0 417 18646
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01218736
X-RAY DIFFRACTIONr_bond_other_d0.0030.01617104
X-RAY DIFFRACTIONr_angle_refined_deg1.3181.65525333
X-RAY DIFFRACTIONr_angle_other_deg0.4651.56840043
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.92952238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.183563
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.059103375
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1230.22681
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0220824
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023612
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.6145.2668979
X-RAY DIFFRACTIONr_mcbond_other3.6145.2668979
X-RAY DIFFRACTIONr_mcangle_it5.5077.88411208
X-RAY DIFFRACTIONr_mcangle_other5.5077.88511209
X-RAY DIFFRACTIONr_scbond_it3.7315.5639757
X-RAY DIFFRACTIONr_scbond_other3.735.5649758
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8468.20714126
X-RAY DIFFRACTIONr_long_range_B_refined8.19963.97121020
X-RAY DIFFRACTIONr_long_range_B_other8.18363.95120952
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.42→2.482 Å
RfactorNum. reflection% reflection
Rfree0.361 386 -
Rwork0.371 7752 -
obs--98.76 %

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