[English] 日本語
Yorodumi
- PDB-7yc4: Acetylesterase (LgEstI) F207A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7yc4
TitleAcetylesterase (LgEstI) F207A
ComponentsAlpha/beta hydrolase
KeywordsHYDROLASE / Esterase / Lipase / pathogen bacteria
Function / homology:
Function and homology information
Biological speciesLactococcus garvieae subsp. garvieae (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsDo, H. / Lee, J.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2021M1A5A1075524 Korea, Republic Of
CitationJournal: Plos One / Year: 2023
Title: Crystal structure and biochemical analysis of acetylesterase (LgEstI) from Lactococcus garvieae.
Authors: Do, H. / Yoo, W. / Wang, Y. / Nam, Y. / Shin, S.C. / Kim, H.W. / Kim, K.K. / Lee, J.H.
History
DepositionJun 30, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alpha/beta hydrolase
B: Alpha/beta hydrolase
C: Alpha/beta hydrolase
D: Alpha/beta hydrolase
E: Alpha/beta hydrolase
F: Alpha/beta hydrolase
G: Alpha/beta hydrolase
H: Alpha/beta hydrolase


Theoretical massNumber of molelcules
Total (without water)290,1808
Polymers290,1808
Non-polymers00
Water10,395577
1
A: Alpha/beta hydrolase
G: Alpha/beta hydrolase


Theoretical massNumber of molelcules
Total (without water)72,5452
Polymers72,5452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alpha/beta hydrolase
H: Alpha/beta hydrolase


Theoretical massNumber of molelcules
Total (without water)72,5452
Polymers72,5452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Alpha/beta hydrolase
D: Alpha/beta hydrolase


Theoretical massNumber of molelcules
Total (without water)72,5452
Polymers72,5452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
E: Alpha/beta hydrolase
F: Alpha/beta hydrolase


Theoretical massNumber of molelcules
Total (without water)72,5452
Polymers72,5452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.200, 127.390, 104.760
Angle α, β, γ (deg.)90.000, 90.173, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Alpha/beta hydrolase


Mass: 36272.551 Da / Num. of mol.: 8 / Mutation: F207A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus garvieae subsp. garvieae (lactic acid bacteria)
Gene: F4V47_03290 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5M9R5N4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 577 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 46.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2M Potassium Formate, pH 7.3, 20% (w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→29.365 Å / Num. obs: 151387 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.997 / Net I/σ(I): 10.7
Reflection shellResolution: 2.1→2.14 Å / Rmerge(I) obs: 0.712 / Num. unique obs: 7500

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7YC0

7yc0


Resolution: 2.1→29.365 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.923 / SU B: 5.972 / SU ML: 0.156 / Cross valid method: FREE R-VALUE / ESU R: 0.239 / ESU R Free: 0.199
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2451 7581 5.008 %
Rwork0.1919 143805 -
all0.195 --
obs-151386 99.887 %
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: 36.435 Å2
Baniso -1Baniso -2Baniso -3
1--0.015 Å20 Å20.001 Å2
2--0.01 Å20 Å2
3---0.005 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.365 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20140 0 0 577 20717
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01320556
X-RAY DIFFRACTIONr_bond_other_d0.0010.01719145
X-RAY DIFFRACTIONr_angle_refined_deg1.5381.64227917
X-RAY DIFFRACTIONr_angle_other_deg1.2811.57944008
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4152511
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.71423.2551198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.884153488
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8915128
X-RAY DIFFRACTIONr_chiral_restr0.0730.22703
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0223593
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024775
X-RAY DIFFRACTIONr_nbd_refined0.1990.24435
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1780.219200
X-RAY DIFFRACTIONr_nbtor_refined0.160.29846
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.210240
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2883
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0970.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2420.224
X-RAY DIFFRACTIONr_nbd_other0.2530.296
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1470.216
X-RAY DIFFRACTIONr_mcbond_it2.6573.72410068
X-RAY DIFFRACTIONr_mcbond_other2.6573.72310067
X-RAY DIFFRACTIONr_mcangle_it3.6055.57312571
X-RAY DIFFRACTIONr_mcangle_other3.6065.57312572
X-RAY DIFFRACTIONr_scbond_it3.054.04410488
X-RAY DIFFRACTIONr_scbond_other3.0514.04410489
X-RAY DIFFRACTIONr_scangle_it4.5845.95515346
X-RAY DIFFRACTIONr_scangle_other4.5845.95515347
X-RAY DIFFRACTIONr_lrange_it5.73243.70223056
X-RAY DIFFRACTIONr_lrange_other5.72643.67822998
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.1550.3135660.25710604X-RAY DIFFRACTION100
2.155-2.2140.36170.2410275X-RAY DIFFRACTION100
2.214-2.2780.3096340.2329972X-RAY DIFFRACTION99.9906
2.278-2.3480.2854990.2229742X-RAY DIFFRACTION100
2.348-2.4250.2854450.2199552X-RAY DIFFRACTION100
2.425-2.510.2764410.2029189X-RAY DIFFRACTION99.9689
2.51-2.6040.2774270.2068933X-RAY DIFFRACTION99.9253
2.604-2.7110.2614040.2058528X-RAY DIFFRACTION99.8882
2.711-2.8310.284260.2058221X-RAY DIFFRACTION99.9422
2.831-2.9690.273930.2057764X-RAY DIFFRACTION100
2.969-3.130.2863980.2247419X-RAY DIFFRACTION99.9872
3.13-3.3190.2573930.2117038X-RAY DIFFRACTION99.9865
3.319-3.5480.2553460.2066620X-RAY DIFFRACTION99.9426
3.548-3.8320.2353160.1846162X-RAY DIFFRACTION99.8459
3.832-4.1970.2143130.1625648X-RAY DIFFRACTION99.7323
4.197-4.6920.1862600.1475149X-RAY DIFFRACTION99.8339
4.692-5.4160.1972680.1634479X-RAY DIFFRACTION99.3304
5.416-6.6290.2071870.1643896X-RAY DIFFRACTION99.8777
6.629-9.3560.1841540.1472979X-RAY DIFFRACTION99.9043
9.356-29.3650.209940.1751635X-RAY DIFFRACTION96.3768

+
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