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- PDB-7nb5: Structure of EstD11 S144A in complex with naproxen p-nitrophenol ester -

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Basic information

Entry
Database: PDB / ID: 7nb5
TitleStructure of EstD11 S144A in complex with naproxen p-nitrophenol ester
ComponentsEstD11 S144A
KeywordsHYDROLASE / Esterase Hormone-Sensitive Lipase Metagenome library Crystal structure
Function / homologyChem-U68
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 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
DepositionJan 25, 2021Deposition 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 1.3Nov 29, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond / pdbx_database_related
Item: _pdbx_database_related.db_name
Revision 1.4Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EstD11 S144A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3922
Polymers32,0391
Non-polymers3531
Water1,78399
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11700 Å2
Unit cell
Length a, b, c (Å)47.999, 89.705, 125.762
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-403-

HOH

21A-420-

HOH

31A-488-

HOH

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Components

#1: Protein EstD11 S144A


Mass: 32038.812 Da / Num. of mol.: 1
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-U68 / (4-nitrophenyl) (2~{S})-2-(6-methoxynaphthalen-2-yl)propanoate


Mass: 353.369 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H19NO5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.11 Å3/Da / Density % sol: 41.78 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: Sodium formate 3.2M and citrate pH 5 0.1M

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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: Nov 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.13→44.84 Å / Num. obs: 15581 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.027 / Net I/σ(I): 18.2
Reflection shellResolution: 2.13→2.19 Å / Rmerge(I) obs: 0.231 / Mean I/σ(I) obs: 8.2 / Num. unique obs: 1265 / CC1/2: 0.989 / Rpim(I) all: 0.09 / % 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: 7AT0

7at0


Resolution: 2.13→42.36 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.931 / SU B: 11.629 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.244 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.22773 768 4.9 %RANDOM
Rwork0.16738 ---
obs0.17027 14812 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.253 Å2
Baniso -1Baniso -2Baniso -3
1--2.33 Å20 Å20 Å2
2--4.43 Å20 Å2
3----2.09 Å2
Refinement stepCycle: LAST / Resolution: 2.13→42.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2247 0 26 99 2372
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0182335
X-RAY DIFFRACTIONr_bond_other_d0.0010.022226
X-RAY DIFFRACTIONr_angle_refined_deg1.2371.9063190
X-RAY DIFFRACTIONr_angle_other_deg1.0492.9385125
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.25296
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.46522.57797
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.87515369
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0411526
X-RAY DIFFRACTIONr_chiral_restr0.0740.2361
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022619
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02469
X-RAY DIFFRACTIONr_mcbond_it6.2631.3381184
X-RAY DIFFRACTIONr_mcbond_other6.2651.3331183
X-RAY DIFFRACTIONr_mcangle_it7.4921.9721480
X-RAY DIFFRACTIONr_mcangle_other7.5151.9761481
X-RAY DIFFRACTIONr_scbond_it10.7731.9941150
X-RAY DIFFRACTIONr_scbond_other10.7691.9961151
X-RAY DIFFRACTIONr_scangle_other13.1772.7171710
X-RAY DIFFRACTIONr_long_range_B_refined13.99117.9772661
X-RAY DIFFRACTIONr_long_range_B_other14.02617.8322649
LS refinement shellResolution: 2.13→2.185 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 65 -
Rwork0.167 1081 -
obs--99.91 %
Refinement TLS params.Method: refined / Origin x: 13.576 Å / Origin y: 19.592 Å / Origin z: 16.272 Å
111213212223313233
T0.1173 Å20.0426 Å2-0.0042 Å2-0.2069 Å2-0.08 Å2--0.0684 Å2
L3.9291 °2-0.3068 °20.0194 °2-0.8602 °20.2854 °2--2.1733 °2
S0.1293 Å °0.649 Å °-0.0618 Å °-0.0644 Å °-0.1084 Å °0.0678 Å °0.0142 Å °-0.1875 Å °-0.0209 Å °

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