[English] 日本語
Yorodumi
- PDB-5d8m: Crystal structure of the metagenomic carboxyl esterase MGS0156 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5d8m
TitleCrystal structure of the metagenomic carboxyl esterase MGS0156
ComponentsMetagenomic carboxyl esterase MGS0156
KeywordsHYDROLASE / esterase
Function / homologyAlpha/Beta hydrolase fold / membrane / Alpha/beta hydrolase
Function and homology information
Biological speciesuncultured organism (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsCui, H. / Nocek, B. / Tchigvintsev, A. / Popovic, A. / Savchenko, A. / Joachimiak, A. / Yakunin, A.
Funding support Canada, 1items
OrganizationGrant numberCountry
Genome Canada and Ontario Genomics InstituteBEEM project Canada
CitationJournal: To Be Published
Title: Crystal structure of esterase (MGS0156)
Authors: Nocek, B. / Cui, H. / Tchigvintsev, A. / Popovic, A. / Savchenko, A. / Joachimiak, A. / Yakunin, A.
History
DepositionAug 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Metagenomic carboxyl esterase MGS0156


Theoretical massNumber of molelcules
Total (without water)37,0851
Polymers37,0851
Non-polymers00
Water5,729318
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Metagenomic carboxyl esterase MGS0156

A: Metagenomic carboxyl esterase MGS0156


Theoretical massNumber of molelcules
Total (without water)74,1692
Polymers74,1692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x,y,-z+11
Buried area4100 Å2
ΔGint-32 kcal/mol
Surface area24590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.764, 95.907, 135.604
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

-
Components

#1: Protein Metagenomic carboxyl esterase MGS0156


Mass: 37084.516 Da / Num. of mol.: 1 / Fragment: UNP residues 75-421
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured organism (environmental samples)
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0G3FEJ8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.05 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1M Sodium Citrate ph5.6, 0.2M Ammonium Acetate, 30%PEG4K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 10, 2014
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.95→36.06 Å / Num. obs: 27606 / % possible obs: 95.7 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 20
Reflection shellResolution: 1.95→1.98 Å

-
Processing

Software
NameVersionClassification
PHENIXdev_1888refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.95→36.06 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1898 2268 5.05 %
Rwork0.1512 --
obs0.1532 26361 91.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→36.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2461 0 0 318 2779
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012538
X-RAY DIFFRACTIONf_angle_d1.163473
X-RAY DIFFRACTIONf_dihedral_angle_d10.924924
X-RAY DIFFRACTIONf_chiral_restr0.054406
X-RAY DIFFRACTIONf_plane_restr0.006456
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9496-1.9920.2178660.18611485X-RAY DIFFRACTION45
1.992-2.03830.21571100.17641775X-RAY DIFFRACTION55
2.0383-2.08930.2021130.17442058X-RAY DIFFRACTION63
2.0893-2.14580.21271410.17152298X-RAY DIFFRACTION70
2.1458-2.20890.21081290.16572526X-RAY DIFFRACTION78
2.2089-2.28020.23031210.16022724X-RAY DIFFRACTION83
2.2802-2.36170.22261570.14842812X-RAY DIFFRACTION88
2.3617-2.45620.18071830.15072956X-RAY DIFFRACTION91
2.4562-2.5680.19611380.14853040X-RAY DIFFRACTION93
2.568-2.70330.18851590.16123093X-RAY DIFFRACTION94
2.7033-2.87260.20431820.1623031X-RAY DIFFRACTION94
2.8726-3.09430.19561650.16013072X-RAY DIFFRACTION94
3.0943-3.40550.21551610.14583047X-RAY DIFFRACTION93
3.4055-3.89780.17381470.13232992X-RAY DIFFRACTION92
3.8978-4.90880.14521550.13142961X-RAY DIFFRACTION90
4.9088-36.06170.17681430.15512784X-RAY DIFFRACTION85
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.3519-0.0477-1.46190.51480.31552.3422-0.01860.0467-0.0123-0.00780.0139-0.05330.2343-0.0598-0.00210.10630.0256-0.00660.17390.0270.10746.158620.79260.5719
21.2705-0.0842-0.44630.84920.28051.5463-0.0589-0.03180.001-0.11850.0156-0.10320.12290.30510.03290.13780.01920.0290.11630.01110.114712.364523.280744.0745
32.43330.04320.05871.4056-0.52472.4706-0.01580.0838-0.1341-0.1036-0.00320.15790.2232-0.2260.03180.0958-0.0302-0.00750.08420.00620.1158-3.459919.099145.9462
41.2988-0.11730.75143.8941-4.3177.7982-0.1417-0.13990.27590.28910.39480.5014-0.6808-0.8104-0.26930.17760.01830.00630.2702-0.02770.244-11.488731.915650.4709
51.5763-0.1188-0.54021.8758-0.24672.3454-0.0524-0.17320.05380.10980.1251-0.0172-0.04840.1123-0.06340.06110.0090.01420.12570.00390.06485.931527.631457.5418
62.1057-0.9785-0.28954.82360.7881.95760.1339-0.00780.2014-0.4735-0.1229-0.1622-0.15080.23530.01890.0968-0.00530.02130.1275-0.01240.077112.23328.799945.4786
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 82 through 121)
2X-RAY DIFFRACTION2chain 'A' and (resid 122 through 205 )
3X-RAY DIFFRACTION3chain 'A' and (resid 206 through 272 )
4X-RAY DIFFRACTION4chain 'A' and (resid 273 through 310 )
5X-RAY DIFFRACTION5chain 'A' and (resid 311 through 372 )
6X-RAY DIFFRACTION6chain 'A' and (resid 373 through 413 )

+
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