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- PDB-7at3: Structure of EstD11 in complex with Naproxen and methanol -

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Basic information

Entry
Database: PDB / ID: 7at3
TitleStructure of EstD11 in complex with Naproxen and methanol
ComponentsEstD11
KeywordsHYDROLASE / Esterase Hormone-Sensitive Lipase Metagenome library Crystal structure
Function / homologyFORMIC ACID / METHANOL / (2R)-2-(6-methoxynaphthalen-2-yl)propanoic acid
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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 / 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
B: EstD11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,31115
Polymers64,3722
Non-polymers93913
Water13,313739
1
A: EstD11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7249
Polymers32,1861
Non-polymers5388
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: EstD11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5866
Polymers32,1861
Non-polymers4005
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.054, 80.487, 145.055
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


Mass: 32186.012 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.: 9 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-NPX / (2R)-2-(6-methoxynaphthalen-2-yl)propanoic acid / (R)-Naproxen


Mass: 230.259 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H14O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MOH / METHANOL


Mass: 32.042 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH4O / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 739 / 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: 2.18 Å3/Da / Density % sol: 43.55 %
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: Oct 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.4→48.35 Å / Num. obs: 111559 / % possible obs: 100 % / Redundancy: 9.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.034 / Net I/σ(I): 10.5
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 9.8 % / Rmerge(I) obs: 1.155 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 5471 / CC1/2: 0.66 / Rpim(I) all: 0.383 / % possible all: 99.9

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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: 1.4→45.66 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.112 / SU ML: 0.043 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.06 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1859 5631 5.1 %RANDOM
Rwork0.1621 ---
obs0.1634 105827 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.87 Å2 / Biso mean: 18.398 Å2 / Biso min: 9.76 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2---0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 1.4→45.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4494 0 65 739 5298
Biso mean--33.72 36.88 -
Num. residues----590
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0134960
X-RAY DIFFRACTIONr_bond_other_d0.0040.0174818
X-RAY DIFFRACTIONr_angle_refined_deg1.4171.6476793
X-RAY DIFFRACTIONr_angle_other_deg1.3831.57311060
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5895656
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.39319.552268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.18915810
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8081560
X-RAY DIFFRACTIONr_chiral_restr0.0760.2635
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025781
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021155
Refine LS restraints NCS

Ens-ID: 1 / Number: 9856 / 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: 1.4→1.436 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 411 -
Rwork0.287 7723 -
all-8134 -
obs--99.95 %

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