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- PDB-4ftw: Crystal structure of a carboxyl esterase N110C/L145H at 2.3 angst... -

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Basic information

Entry
Database: PDB / ID: 4ftw
TitleCrystal structure of a carboxyl esterase N110C/L145H at 2.3 angstrom resolution
ComponentsPhospholipase/Carboxylesterase
KeywordsHYDROLASE / alpha/beta hydrolase superfamily / esterase
Function / homology
Function and homology information


: / Phospholipase/carboxylesterase/thioesterase / Phospholipase/Carboxylesterase / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-3CM / Phospholipase/Carboxylesterase
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWu, L. / Ma, J. / Zhou, J. / Yu, H.
CitationJournal: Appl.Microbiol.Biotechnol. / Year: 2013
Title: Enhanced enantioselectivity of a carboxyl esterase from Rhodobacter sphaeroides by directed evolution.
Authors: Ma, J. / Wu, L. / Guo, F. / Gu, J. / Tang, X. / Jiang, L. / Liu, J. / Zhou, J. / Yu, H.
History
DepositionJun 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1May 29, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phospholipase/Carboxylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7475
Polymers29,9201
Non-polymers8274
Water39622
1
A: Phospholipase/Carboxylesterase
hetero molecules

A: Phospholipase/Carboxylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,49410
Polymers59,8402
Non-polymers1,6558
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area1990 Å2
ΔGint-6 kcal/mol
Surface area17390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.382, 112.382, 47.569
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Phospholipase/Carboxylesterase


Mass: 29919.902 Da / Num. of mol.: 1 / Mutation: N110C/L145H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Strain: ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158 / Gene: CGMCC1.1737, RHOS4_13150, RSP_2728 / Plasmid: pET-30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q3J2V1, carboxylesterase
#3: Sugar ChemComp-3CM / 3-CYCLOHEXYLPROPYL 4-O-ALPHA-D-GLUCOPYRANOSYL-BETA-D-GLUCOPYRANOSIDE / CYMAL-3


Type: D-saccharide / Mass: 466.520 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C21H38O11

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Non-polymers , 4 types, 25 molecules

#2: Chemical ChemComp-PIN / PIPERAZINE-N,N'-BIS(2-ETHANESULFONIC ACID) / PIPES / 1,4-PIPERAZINEDIETHANESULFONIC ACID


Mass: 302.368 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O6S2 / Comment: pH buffer*YM
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.49 Å3/Da / Density % sol: 64.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 1.3M Na-tartrate, 34.5mM CYMAL-3, 0.1M pipes , pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 15208 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.8 % / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 20.538
Reflection shell
Resolution (Å)Redundancy (%)Diffraction-ID% possible all
2.3-2.3810.31100
2.38-2.4810.31100
2.48-2.5910.31100
2.59-2.7310.31100
2.73-2.910.31100
2.9-3.1210.31100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERMRphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4FHZ

4fhz


Resolution: 2.3→48.663 Å / SU ML: 0.35 / Isotropic thermal model: Isotropic / σ(F): 0 / Phase error: 26.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2991 757 4.98 %RANDOM
Rwork0.2389 ---
obs0.2416 15208 97.36 %-
all-15175 --
Solvent computationShrinkage radii: 0.49 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 72.139 Å2 / ksol: 0.387 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.891 Å2-0 Å20 Å2
2---7.891 Å2-0 Å2
3---15.7821 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.663 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1611 0 52 22 1685
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071699
X-RAY DIFFRACTIONf_angle_d1.2192314
X-RAY DIFFRACTIONf_dihedral_angle_d18.158672
X-RAY DIFFRACTIONf_chiral_restr0.077255
X-RAY DIFFRACTIONf_plane_restr0.004302
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.47680.3261660.28512892X-RAY DIFFRACTION100
2.4768-2.72610.32591510.26662947X-RAY DIFFRACTION100
2.7261-3.12050.29261730.25062936X-RAY DIFFRACTION100
3.1205-3.93120.32251460.22112930X-RAY DIFFRACTION98
3.9312-48.67370.27841210.23672746X-RAY DIFFRACTION89

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