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- PDB-7at0: Structure of the Hormone-Sensitive Lipase like EstD11 -

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Basic information

Entry
Database: PDB / ID: 7at0
TitleStructure of the Hormone-Sensitive Lipase like EstD11
ComponentsEstD11
KeywordsHYDROLASE / Esterase Hormone-Sensitive Lipase Metagenome library Crystal structure
Function / homologyFORMIC ACID / PHENOL
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsMiguel-Ruano, V. / Rivera, I. / Hermoso, J.A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2017-90030-P Spain
CitationJournal: Comput Struct Biotechnol J / Year: 2021
Title: Biochemical and Structural Characterization of a novel thermophilic esterase EstD11 provide catalytic insights for the HSL family.
Authors: Miguel-Ruano, V. / Rivera, I. / Rajkovic, J. / Knapik, K. / Torrado, A. / Otero, J.M. / Beneventi, E. / Becerra, M. / Sanchez-Costa, M. / Hidalgo, A. / Berenguer, J. / Gonzalez-Siso, M.I. / ...Authors: Miguel-Ruano, V. / Rivera, I. / Rajkovic, J. / Knapik, K. / Torrado, A. / Otero, J.M. / Beneventi, E. / Becerra, M. / Sanchez-Costa, M. / Hidalgo, A. / Berenguer, J. / Gonzalez-Siso, M.I. / Cruces, J. / Rua, M.L. / Hermoso, J.A.
History
DepositionOct 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 17, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 2, 2022Group: Data collection / Database references / Category: database_2 / diffrn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn.ambient_temp
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EstD11
B: EstD11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,61812
Polymers64,1102
Non-polymers50810
Water10,647591
1
A: EstD11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3797
Polymers32,0551
Non-polymers3246
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: EstD11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2395
Polymers32,0551
Non-polymers1844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.883, 80.168, 144.989
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein EstD11


Mass: 32054.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-IPH / PHENOL


Mass: 94.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 591 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.16 Å3/Da / Density % sol: 43.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 3,2M Sodium formate + 0,1M citrate pH 5.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.2→48.33 Å / Num. obs: 174770 / % possible obs: 100 % / Redundancy: 12.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.034 / Rrim(I) all: 0.123 / Net I/σ(I): 11.3 / Num. measured all: 2259919 / Scaling rejects: 2
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 12.4 % / Rmerge(I) obs: 0.994 / Num. unique obs: 8521 / CC1/2: 0.733 / Rpim(I) all: 0.292 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XVC

4xvc


Resolution: 1.2→45.51 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.978 / SU B: 1.227 / SU ML: 0.024 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.15049 8727 5 %RANDOM
Rwork0.12266 ---
obs0.12404 165932 99.99 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.3 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.314 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20 Å2
2--0.1 Å2-0 Å2
3----0.33 Å2
Refinement stepCycle: LAST / Resolution: 1.2→45.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4486 0 34 591 5111
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0185133
X-RAY DIFFRACTIONr_bond_other_d0.0010.024892
X-RAY DIFFRACTIONr_angle_refined_deg1.5811.897061
X-RAY DIFFRACTIONr_angle_other_deg1.2642.93111311
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5485696
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.59922.701211
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.43215838
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.051557
X-RAY DIFFRACTIONr_chiral_restr0.1110.2798
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026017
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021052
X-RAY DIFFRACTIONr_mcbond_it1.5911.3352646
X-RAY DIFFRACTIONr_mcbond_other1.6031.3372647
X-RAY DIFFRACTIONr_mcangle_it1.992.0123388
X-RAY DIFFRACTIONr_mcangle_other22.0133389
X-RAY DIFFRACTIONr_scbond_it2.9051.7042487
X-RAY DIFFRACTIONr_scbond_other2.7941.692476
X-RAY DIFFRACTIONr_scangle_other3.3642.4223674
X-RAY DIFFRACTIONr_long_range_B_refined3.718.2855988
X-RAY DIFFRACTIONr_long_range_B_other3.33217.5135828
X-RAY DIFFRACTIONr_rigid_bond_restr2.541310025
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 636 -
Rwork0.218 12147 -
obs--99.98 %

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