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- PDB-7av5: Structure of EstD11 in complex with Fluorescein -

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Basic information

Entry
Database: PDB / ID: 7av5
TitleStructure of EstD11 in complex with Fluorescein
ComponentsEstD11
KeywordsHYDROLASE / Esterase Hormone-Sensitive Lipase Metagenome library Crystal structure
Function / homologyACETATE ION / FLUORESCIN / FORMIC ACID
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 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
DepositionNov 4, 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
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: EstD11
BBB: EstD11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,90610
Polymers64,3722
Non-polymers1,5348
Water7,494416
1
AAA: EstD11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0066
Polymers32,1861
Non-polymers8205
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: EstD11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9014
Polymers32,1861
Non-polymers7153
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.278, 80.562, 145.788
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain: (Details: Chains AAA BBB)

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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)
Plasmid: pET22 / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical
ChemComp-FDS / FLUORESCIN / Fluorescein


Mass: 334.322 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H14O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 416 / 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: 2.2 Å3/Da / Density % sol: 44.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 3.2M Sodium formate and 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: Jul 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.97→45.872 Å / Num. obs: 41145 / % possible obs: 100 % / Redundancy: 6.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.045 / Net I/σ(I): 15.5
Reflection shellResolution: 1.97→2.02 Å / Redundancy: 7 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 2857 / CC1/2: 0.789 / Rpim(I) all: 0.329 / % 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: 1.97→45.872 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.933 / WRfactor Rfree: 0.191 / WRfactor Rwork: 0.15 / SU B: 4.015 / SU ML: 0.111 / Average fsc free: 0.9295 / Average fsc work: 0.9402 / Cross valid method: FREE R-VALUE / ESU R: 0.176 / ESU R Free: 0.154
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2144 2099 5.11 %
Rwork0.1696 38980 -
all0.172 --
obs-41079 99.964 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 22.754 Å2
Baniso -1Baniso -2Baniso -3
1--0.002 Å2-0 Å20 Å2
2---0.006 Å20 Å2
3---0.008 Å2
Refinement stepCycle: LAST / Resolution: 1.97→45.872 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4461 0 113 416 4990
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0134723
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174444
X-RAY DIFFRACTIONr_angle_refined_deg1.5451.6796458
X-RAY DIFFRACTIONr_angle_other_deg1.3621.5810234
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.85593
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.45120.083242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.19815738
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9671550
X-RAY DIFFRACTIONr_chiral_restr0.0750.2599
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025369
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02993
X-RAY DIFFRACTIONr_nbd_refined0.2170.2994
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.24333
X-RAY DIFFRACTIONr_nbtor_refined0.160.22329
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.22043
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2368
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1310.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2890.228
X-RAY DIFFRACTIONr_nbd_other0.2070.282
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2660.223
X-RAY DIFFRACTIONr_mcbond_it1.9172.1212367
X-RAY DIFFRACTIONr_mcbond_other1.9172.1222368
X-RAY DIFFRACTIONr_mcangle_it2.8733.162961
X-RAY DIFFRACTIONr_mcangle_other2.8733.1622962
X-RAY DIFFRACTIONr_scbond_it3.1492.642356
X-RAY DIFFRACTIONr_scbond_other3.1462.6392354
X-RAY DIFFRACTIONr_scangle_it4.8053.8093497
X-RAY DIFFRACTIONr_scangle_other4.8043.813498
X-RAY DIFFRACTIONr_lrange_it6.67127.3885621
X-RAY DIFFRACTIONr_lrange_other6.48126.9055497
X-RAY DIFFRACTIONr_ncsr_local_group_10.0980.059376
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.0210.2871660.2692827X-RAY DIFFRACTION99.9332
2.021-2.0760.2721600.2432739X-RAY DIFFRACTION99.9655
2.076-2.1370.2431400.2172708X-RAY DIFFRACTION99.8597
2.137-2.2020.2281430.1882615X-RAY DIFFRACTION100
2.202-2.2750.2111140.172547X-RAY DIFFRACTION99.9624
2.275-2.3540.2511210.1812470X-RAY DIFFRACTION99.9614
2.354-2.4430.2161380.1632380X-RAY DIFFRACTION99.9603
2.443-2.5430.1881270.1582287X-RAY DIFFRACTION99.9586
2.543-2.6560.2451190.1642181X-RAY DIFFRACTION100
2.656-2.7850.2041110.1712125X-RAY DIFFRACTION100
2.785-2.9350.2291060.1792016X-RAY DIFFRACTION100
2.935-3.1130.255950.1841912X-RAY DIFFRACTION100
3.113-3.3280.217960.1651797X-RAY DIFFRACTION100
3.328-3.5940.171850.1461681X-RAY DIFFRACTION100
3.594-3.9360.174750.1411577X-RAY DIFFRACTION100
3.936-4.3990.187880.1341410X-RAY DIFFRACTION100
4.399-5.0760.17720.1391244X-RAY DIFFRACTION100
5.076-6.2090.212660.1541098X-RAY DIFFRACTION100
6.209-8.750.232410.157857X-RAY DIFFRACTION100
8.75-45.8720.206360.19510X-RAY DIFFRACTION99.2727

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