[English] 日本語
Yorodumi
- PDB-7at4: Structure of EstD11 in complex with Naproxen -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7at4
TitleStructure of EstD11 in complex with Naproxen
ComponentsEstD11
KeywordsHYDROLASE / Esterase Hormone-Sensitive Lipase Metagenome library Crystal structure
Function / homologyFORMIC ACID / (2R)-2-(6-methoxynaphthalen-2-yl)propanoic acid
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: EstD11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,38311
Polymers32,1861
Non-polymers1,19710
Water5,441302
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.172, 90.604, 126.251
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-1703-

HOH

21A-1710-

HOH

31A-1830-

HOH

41A-1925-

HOH

-
Components

#1: Protein EstD11


Mass: 32186.012 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Metagenomic library
Source: (gene. exp.) uncultured bacterium (environmental samples)
Plasmid: pET22 / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 6 / 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.: 4 / Source method: obtained synthetically / Formula: C14H14O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 3.2M Sodium formate + 0.1M citrate pH 5

-
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 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→45.3 Å / Num. obs: 30890 / % possible obs: 100 % / Redundancy: 13.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.031 / Net I/σ(I): 18.9
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 12.6 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 1652 / CC1/2: 0.91 / Rpim(I) all: 0.277 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7AT0

7at0


Resolution: 1.7→45.048 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.105 / SU ML: 0.069 / Cross valid method: FREE R-VALUE / ESU R: 0.103 / ESU R Free: 0.1
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1908 1548 5.013 %
Rwork0.156 29330 -
all0.158 --
obs-30878 99.948 %
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: 19.281 Å2
Baniso -1Baniso -2Baniso -3
1--0.012 Å20 Å20 Å2
2--0.011 Å2-0 Å2
3---0.001 Å2
Refinement stepCycle: LAST / Resolution: 1.7→45.048 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2243 0 86 302 2631
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132435
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172301
X-RAY DIFFRACTIONr_angle_refined_deg1.7121.6453322
X-RAY DIFFRACTIONr_angle_other_deg1.461.5695301
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9015306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.8920.159126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.40315383
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.2041526
X-RAY DIFFRACTIONr_chiral_restr0.0920.2309
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022795
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02523
X-RAY DIFFRACTIONr_nbd_refined0.2230.2525
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.22309
X-RAY DIFFRACTIONr_nbtor_refined0.1680.21195
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.21136
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2050.2258
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0660.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2650.227
X-RAY DIFFRACTIONr_nbd_other0.2440.255
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2170.226
X-RAY DIFFRACTIONr_mcbond_it1.6771.6851203
X-RAY DIFFRACTIONr_mcbond_other1.6781.6891204
X-RAY DIFFRACTIONr_mcangle_it2.3992.5251510
X-RAY DIFFRACTIONr_mcangle_other2.4022.5281511
X-RAY DIFFRACTIONr_scbond_it3.2472.1881230
X-RAY DIFFRACTIONr_scbond_other3.2482.1881229
X-RAY DIFFRACTIONr_scangle_it4.863.1061808
X-RAY DIFFRACTIONr_scangle_other4.8583.1061809
X-RAY DIFFRACTIONr_lrange_it6.70722.7212944
X-RAY DIFFRACTIONr_lrange_other6.49421.7942838
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.7440.3041160.2392160X-RAY DIFFRACTION99.9122
1.744-1.7920.2441030.2082077X-RAY DIFFRACTION99.9542
1.792-1.8440.2451160.1982022X-RAY DIFFRACTION99.9065
1.844-1.9010.219870.1791979X-RAY DIFFRACTION100
1.901-1.9630.195930.1651919X-RAY DIFFRACTION100
1.963-2.0320.2930.1571869X-RAY DIFFRACTION99.9491
2.032-2.1080.1871020.1511788X-RAY DIFFRACTION99.9471
2.108-2.1940.22870.1471720X-RAY DIFFRACTION99.9447
2.194-2.2920.182830.141650X-RAY DIFFRACTION100
2.292-2.4040.207810.1421609X-RAY DIFFRACTION100
2.404-2.5330.179830.1471508X-RAY DIFFRACTION100
2.533-2.6870.201830.1611415X-RAY DIFFRACTION100
2.687-2.8720.194980.1581325X-RAY DIFFRACTION99.9298
2.872-3.1020.18600.161272X-RAY DIFFRACTION100
3.102-3.3970.182600.1551173X-RAY DIFFRACTION100
3.397-3.7970.152520.1371062X-RAY DIFFRACTION100
3.797-4.3830.183490.127947X-RAY DIFFRACTION100
4.383-5.3630.137480.134811X-RAY DIFFRACTION99.8837
5.363-7.5640.189320.167642X-RAY DIFFRACTION100
7.564-45.0480.21220.182382X-RAY DIFFRACTION98.5366

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more