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- PDB-4rnc: Crystal structure of an esterase RhEst1 from Rhodococcus sp. ECU1013 -

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Basic information

Entry
Database: PDB / ID: 4rnc
TitleCrystal structure of an esterase RhEst1 from Rhodococcus sp. ECU1013
ComponentsEsterase
KeywordsHYDROLASE / alpha/beta hydrolase fold
Function / homology
Function and homology information


carboxylesterase / carboxylesterase activity / membrane
Similarity search - Function
: / Alpha/beta hydrolase family / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Alpha/beta hydrolase
Similarity search - Component
Biological speciesRhodococcus sp. ECU1013 (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.95 Å
AuthorsDou, S. / Kong, X.D. / Xu, J.H. / Zhou, J.
CitationJournal: CATALYSIS SCIENCE AND TECHNOLOGY / Year: 2015
Title: Substrate channel evolution of an esterase for the synthesis of Cilastatin
Authors: Luan, Z.J. / L Li, F. / Dou, S. / Chen, Q. / Kong, X.D. / Zhou, J. / Yu, H.L. / Xu, J.H.
History
DepositionOct 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Esterase
B: Esterase
C: Esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,5856
Polymers97,3003
Non-polymers2853
Water10,755597
1
A: Esterase
B: Esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,0564
Polymers64,8662
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-24 kcal/mol
Surface area20060 Å2
MethodPISA
2
C: Esterase
hetero molecules

C: Esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,0564
Polymers64,8662
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area2990 Å2
ΔGint-24 kcal/mol
Surface area20020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)212.926, 45.383, 77.443
Angle α, β, γ (deg.)90.000, 105.820, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Esterase


Mass: 32433.229 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus sp. ECU1013 (bacteria) / Strain: ECU1013 isolated from soil / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A088CB91*PLUS
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 597 / 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: 1.85 Å3/Da / Density % sol: 33.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 3 M Na/K Phosphate, 0.1M Tris pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 28, 2013 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 52476 / % possible obs: 100 % / Redundancy: 4 % / Rmerge(I) obs: 0.079 / Χ2: 1.049 / Net I/σ(I): 12.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.95-2.023.80.59451791.0961100
2.02-2.13.90.43352381.089199.9
2.1-2.23.90.3151751.077199.9
2.2-2.3140.23351841.042199.9
2.31-2.4640.19452121.0741100
2.46-2.654.10.15652761.0631100
2.65-2.914.10.11352171.091100
2.91-3.334.10.08152720.9581100
3.33-4.24.20.0652841.083199.9
4.2-504.10.04354390.931100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.8.0049refinement
PDB_EXTRACT3.15data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing
RefinementMethod to determine structure: SAD / Resolution: 1.95→50 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.2176 / WRfactor Rwork: 0.1645 / FOM work R set: 0.8325 / SU B: 4.279 / SU ML: 0.119 / SU R Cruickshank DPI: 0.1715 / SU Rfree: 0.1539 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.171 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2119 2674 5.1 %RANDOM
Rwork0.1608 ---
obs0.1635 52476 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 123.99 Å2 / Biso mean: 34.4 Å2 / Biso min: 19.88 Å2
Baniso -1Baniso -2Baniso -3
1--1.65 Å20 Å20.15 Å2
2--0.48 Å20 Å2
3---0.93 Å2
Refinement stepCycle: LAST / Resolution: 1.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6063 0 12 597 6672
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0196195
X-RAY DIFFRACTIONr_bond_other_d0.0020.025811
X-RAY DIFFRACTIONr_angle_refined_deg1.6921.9518430
X-RAY DIFFRACTIONr_angle_other_deg0.861313317
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4125828
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.03223.253249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.71215900
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7671545
X-RAY DIFFRACTIONr_chiral_restr0.0990.2948
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217224
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021407
X-RAY DIFFRACTIONr_mcbond_it2.7773.2433321
X-RAY DIFFRACTIONr_mcbond_other2.7773.2413320
X-RAY DIFFRACTIONr_mcangle_it3.7274.8484146
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 211 -
Rwork0.261 3591 -
all-3802 -
obs--98.7 %

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