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- PDB-7atd: Structure of inactive EstD11 S144A in complex with methyl-naproxen -

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Basic information

Entry
Database: PDB / ID: 7atd
TitleStructure of inactive EstD11 S144A in complex with methyl-naproxen
ComponentsEstD11 S144A
KeywordsHYDROLASE / Esterase Hormone-Sensitive Lipase Metagenome library Crystal structure
Function / homologyACETATE ION / FORMIC ACID / Naproxen Methyl Ester
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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 29, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 2.0Mar 17, 2021Group: Database references / Non-polymer description / Category: chem_comp / citation
Item: _chem_comp.formula / _citation.journal_volume ..._chem_comp.formula / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.1Feb 2, 2022Group: Data collection / Database references / Category: database_2 / diffrn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn.ambient_temp
Revision 2.2Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EstD11 S144A
B: EstD11 S144A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,34719
Polymers64,3402
Non-polymers1,00717
Water12,124673
1
A: EstD11 S144A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,82715
Polymers32,1701
Non-polymers65714
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: EstD11 S144A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5194
Polymers32,1701
Non-polymers3493
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.846, 80.243, 145.146
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: _ / Auth seq-ID: 2 - 296 / Label seq-ID: 2 - 296

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein EstD11 S144A


Mass: 32170.012 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.: 14 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-RXH / Naproxen Methyl Ester / Methyl (2S)-2-(6-methoxynaphthalen-2-yl)propanoate / (S)-Methyl 2-(6-methoxynaphthalen-2-yl)propanoate / (S)-Naproxen Methyl Ester / methyl-naproxen;


Mass: 244.286 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H16O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 673 / 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: 2.17 Å3/Da / Density % sol: 43.19 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 3.2M Sodium formate + 0.1M citrate pH 5 / PH range: 5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.072 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 1.45→48.38 Å / Num. obs: 99895 / % possible obs: 100 % / Redundancy: 10.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.047 / Net I/σ(I): 8.8
Reflection shellResolution: 1.45→1.47 Å / Redundancy: 10.3 % / Rmerge(I) obs: 1.752 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4827 / CC1/2: 0.53 / Rpim(I) all: 0.57 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7AT0

7at0


Resolution: 1.45→45.48 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.5 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.067 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1915 5071 5.1 %RANDOM
Rwork0.1668 ---
obs0.168 94720 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 84.72 Å2 / Biso mean: 18.971 Å2 / Biso min: 9.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0 Å2
2---0 Å20 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 1.45→45.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4494 0 68 673 5235
Biso mean--36.84 36.03 -
Num. residues----590
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0134878
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174700
X-RAY DIFFRACTIONr_angle_refined_deg1.5261.6516670
X-RAY DIFFRACTIONr_angle_other_deg1.4521.57710795
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9515638
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.02420.236254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.54915781
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2281552
X-RAY DIFFRACTIONr_chiral_restr0.0820.2628
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025677
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021101
Refine LS restraints NCS

Ens-ID: 1 / Number: 9638 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.45→1.488 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 340 -
Rwork0.325 6929 -
all-7269 -
obs--100 %

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