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- PDB-8yfy: CRYSTAL STRUCTURE OF THE EST1 H274D MUTANT AT PH 4.2 -

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Basic information

Entry
Database: PDB / ID: 8yfy
TitleCRYSTAL STRUCTURE OF THE EST1 H274D MUTANT AT PH 4.2
ComponentsCarboxylesterase
KeywordsHYDROLASE / ALPHA/BETA-HYDRORASE FOLD / CARBOXYLESTERASE
Function / homologyLipase, GDXG, putative serine active site / Lipolytic enzymes "G-D-X-G" family, putative serine active site. / carboxylesterase / : / Alpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold / hydrolase activity / Carboxylesterase
Function and homology information
Biological speciesSaccharolobus shibatae (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsUnno, H. / Oshima, Y. / Nishino, T. / Nakayama, T. / Kusunoki, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: J.Biosci.Bioeng. / Year: 2024
Title: Lowering pH optimum of activity of SshEstI, a slightly alkaliphilic archaeal esterase of the hormone-sensitive lipase family.
Authors: Ohara, K. / Oshima, Y. / Unno, H. / Nagano, S. / Kusunoki, M. / Takahashi, S. / Waki, T. / Yamashita, S. / Nakayama, T.
History
DepositionFeb 26, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carboxylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8212
Polymers33,5281
Non-polymers2921
Water4,666259
1
A: Carboxylesterase
hetero molecules

A: Carboxylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,6414
Polymers67,0572
Non-polymers5852
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
Buried area3320 Å2
ΔGint2 kcal/mol
Surface area22360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.096, 71.817, 137.017
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-631-

HOH

21A-750-

HOH

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Components

#1: Protein Carboxylesterase


Mass: 33528.344 Da / Num. of mol.: 1 / Mutation: H274D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharolobus shibatae (archaea) / Gene: SshEstI, J5U21_01394, J5U22_01308 / Plasmid: PTC99A / Production host: Escherichia coli (E. coli) / References: UniProt: Q5NU42, carboxylesterase
#2: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.2 Å3/Da / Density % sol: 42.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.2
Details: 12% PEG 3000, 200 MM NACL, 100 MM PHOSPHATE-CITRATE, PH 4.2, VAPOR DIFFUSION, TEMPERATURE 293K
PH range: 4.2

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Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: IMAGE PLATE / Date: Sep 22, 2003
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.45→18.7 Å / Num. obs: 46275 / % possible obs: 91.5 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 18.15 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 13.6
Reflection shellResolution: 1.45→1.53 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.234 / Mean I/σ(I) obs: 4.6 / Num. unique obs: 46275 / % possible all: 78.6

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMAC5.2.0005refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→18.7 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.964 / SU B: 0.935 / SU ML: 0.037 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.066 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18 2334 5 %RANDOM
Rwork0.155 ---
obs0.156 43939 90.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.65 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.45→18.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2338 0 20 259 2617
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222439
X-RAY DIFFRACTIONr_bond_other_d0.0010.022276
X-RAY DIFFRACTIONr_angle_refined_deg1.3141.9853313
X-RAY DIFFRACTIONr_angle_other_deg0.78135294
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6555301
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.26123.524105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.8215397
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5051516
X-RAY DIFFRACTIONr_chiral_restr0.090.2377
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022690
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02506
X-RAY DIFFRACTIONr_nbd_refined0.2210.2554
X-RAY DIFFRACTIONr_nbd_other0.1810.22481
X-RAY DIFFRACTIONr_nbtor_refined0.190.21280
X-RAY DIFFRACTIONr_nbtor_other0.0830.21398
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2222
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1340.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2470.280
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1810.230
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9141.51926
X-RAY DIFFRACTIONr_mcbond_other0.1641.5611
X-RAY DIFFRACTIONr_mcangle_it1.08522437
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.91331096
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.6624.5873
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.45→1.49 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 136 -
Rwork0.199 2568 -
obs--72.84 %

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