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- PDB-5hc0: Structure of esterase Est22 with p-nitrophenol -

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Basic information

Entry
Database: PDB / ID: 5hc0
TitleStructure of esterase Est22 with p-nitrophenol
ComponentsLipolytic enzyme
KeywordsHYDROLASE / Esterase / Est22
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / hydrolase activity
Similarity search - Function
: / Alpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / P-NITROPHENOL / Lipolytic enzyme
Similarity search - Component
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsLi, J. / Huang, J.
CitationJournal: Sci Rep / Year: 2016
Title: Structural insights of a hormone sensitive lipase homologue Est22.
Authors: Huang, J. / Huo, Y.Y. / Ji, R. / Kuang, S. / Ji, C. / Xu, X.W. / Li, J.
History
DepositionJan 4, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / pdbx_struct_special_symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lipolytic enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7898
Polymers39,0831
Non-polymers7077
Water8,701483
1
A: Lipolytic enzyme
hetero molecules

A: Lipolytic enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,57916
Polymers78,1652
Non-polymers1,41314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Unit cell
Length a, b, c (Å)121.823, 57.220, 54.578
Angle α, β, γ (deg.)90.00, 97.46, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-402-

NPO

21A-920-

HOH

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Components

#1: Protein Lipolytic enzyme


Mass: 39082.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Production host: Escherichia coli (E. coli)
References: UniProt: H6BDX1, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-NPO / P-NITROPHENOL


Mass: 139.109 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5NO3
#4: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 483 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1M MES, pH 5.5, 0.2M Ca(Ac)2, 20% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 72570 / % possible obs: 96.2 % / Redundancy: 6.8 % / Net I/σ(I): 16.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HC4

5hc4


Resolution: 1.4→50 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.967 / SU B: 0.761 / SU ML: 0.03 / Cross valid method: THROUGHOUT / ESU R: 0.048 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15808 3321 5 %RANDOM
Rwork0.13157 ---
obs0.13292 62736 90.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.075 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å2-0.06 Å2
2--0.22 Å2-0 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2534 0 48 483 3065
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0192685
X-RAY DIFFRACTIONr_bond_other_d0.0020.022486
X-RAY DIFFRACTIONr_angle_refined_deg2.3931.9823647
X-RAY DIFFRACTIONr_angle_other_deg1.21435751
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3195354
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.24824.561114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.48815417
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3291516
X-RAY DIFFRACTIONr_chiral_restr0.1520.2396
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0213115
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02581
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_it1.5891.3131384
X-RAY DIFFRACTIONr_mcbond_other1.5681.311382
X-RAY DIFFRACTIONr_mcangle_it2.1451.9631736
X-RAY DIFFRACTIONr_mcangle_other2.1451.9641737
X-RAY DIFFRACTIONr_scbond_it3.0881.5861301
X-RAY DIFFRACTIONr_scbond_other3.0731.5811300
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5252.2721907
X-RAY DIFFRACTIONr_long_range_B_refined8.44613.9453657
X-RAY DIFFRACTIONr_long_range_B_other8.44513.9523658
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.402→1.439 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 164 -
Rwork0.2 3215 -
obs--63.29 %

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