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- PDB-8pc7: STRUCTURE OF ESTER-HYDROLASE EH3 FROM THE METAGENOME OF MARINE SE... -

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Basic information

Entry
Database: PDB / ID: 8pc7
TitleSTRUCTURE OF ESTER-HYDROLASE EH3 FROM THE METAGENOME OF MARINE SEDIMENTS AT MILAZZO HARBOR (SICILY, ITALY) COMPLEXED WITH A DERIVATIVE OF BIPYRIDINE PHOSPHONATE
ComponentsEsterase
KeywordsHYDROLASE / Ester Hydrolase / Complex
Function / homology: / Alpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold / hydrolase activity / DI(HYDROXYETHYL)ETHER / Chem-ZK8 / Esterase
Function and homology information
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsCea-Rama, I. / Sanz-Aparicio, J.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessProject BIO2016-76601-C3-3-R Spain
Spanish Ministry of Economy and CompetitivenessProject PID2019-105838RB-C33 Spain
CitationJournal: Chem.Commun.(Camb.) / Year: 2023
Title: Transforming an esterase into an enantioselective catecholase through bioconjugation of a versatile metal-chelating inhibitor.
Authors: Fernandez-Lopez, L. / Cea-Rama, I. / Alvarez-Malmagro, J. / Ressmann, A.K. / Gonzalez-Alfonso, J.L. / Coscolin, C. / Shahgaldian, P. / Plou, F.J. / Modregger, J. / Pita, M. / Sanz-Aparicio, J. / Ferrer, M.
History
DepositionJun 9, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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
D: Esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,81014
Polymers160,8704
Non-polymers1,94010
Water2,198122
1
A: Esterase
hetero molecules

B: Esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,3206
Polymers80,4352
Non-polymers8854
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area1710 Å2
ΔGint-18 kcal/mol
Surface area25610 Å2
MethodPISA
2
C: Esterase
hetero molecules

D: Esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,4908
Polymers80,4352
Non-polymers1,0556
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area2710 Å2
ΔGint-16 kcal/mol
Surface area25060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.755, 189.390, 75.954
Angle α, β, γ (deg.)90.00, 111.93, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
55
66
/ NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Esterase


Mass: 40217.535 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Production host: Escherichia coli MC1061 (bacteria) / References: UniProt: A0A2K8JN75
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-ZK8 / hexyl-[2-(3-oxidanylpyridin-2-yl)pyridin-3-yl]oxy-phosphinic acid


Mass: 336.323 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H21N2O4P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.36 Å3/Da / Density % sol: 47.84 % / Description: Plaque
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 27% PEG3350, 0.1M Bis-Tris pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979181 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 2, 2020 / Details: KB focusing mirrors
RadiationMonochromator: Si(111) channel-cut, cryocooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979181 Å / Relative weight: 1
ReflectionResolution: 2.4→47.35 Å / Num. obs: 57906 / % possible obs: 100 % / Redundancy: 5.7 % / CC1/2: 0.993 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.057 / Net I/σ(I): 8.1
Reflection shellResolution: 2.4→2.47 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.519 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 4513 / CC1/2: 0.884 / Rpim(I) all: 0.231 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimless0.7.4data scaling
MOLREP11.6.04phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→47.35 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.901 / SU B: 9.65 / SU ML: 0.229 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25293 2927 5.1 %RANDOM
Rwork0.24394 ---
obs0.24438 54940 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.276 Å2
Baniso -1Baniso -2Baniso -3
1-25.04 Å20 Å2-8.31 Å2
2---5.38 Å2-0 Å2
3----19.66 Å2
Refinement stepCycle: 1 / Resolution: 2.4→47.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10266 0 39 124 10429
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01310508
X-RAY DIFFRACTIONr_bond_other_d0.0030.0179892
X-RAY DIFFRACTIONr_angle_refined_deg1.441.65414218
X-RAY DIFFRACTIONr_angle_other_deg1.1931.59322823
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.88851336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.61723.384526
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.463151724
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6041560
X-RAY DIFFRACTIONr_chiral_restr0.0630.21370
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212074
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022322
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_it1.8294.4835365
X-RAY DIFFRACTIONr_mcbond_other1.8294.4835363
X-RAY DIFFRACTIONr_mcangle_it3.0396.726694
X-RAY DIFFRACTIONr_mcangle_other3.0396.726694
X-RAY DIFFRACTIONr_scbond_it1.4414.6235143
X-RAY DIFFRACTIONr_scbond_other1.4414.6235144
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4116.8847525
X-RAY DIFFRACTIONr_long_range_B_refined5.44953.84811626
X-RAY DIFFRACTIONr_long_range_B_other5.44753.85311625
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A105970.08
12B105970.08
21A105650.09
22C105650.09
31A106190.08
32D106190.08
41B106240.07
42C106240.07
51B106510.06
52D106510.06
61C106080.07
62D106080.07
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 228 -
Rwork0.305 4030 -
obs--99.14 %

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