[English] 日本語
Yorodumi
- PDB-2q0s: Structure of the Inhibitor bound form of M. Smegmatis Aryl Esterase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2q0s
TitleStructure of the Inhibitor bound form of M. Smegmatis Aryl Esterase
ComponentsAryl esterase
KeywordsHYDROLASE / SGNH hydrolase / oligomeric enzyme / Acyl Transfer / Aryl Esterase / covalent inhibitor
Function / homologySGNH hydrolase / SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Lipolytic enzyme, G-D-S-L
Function and homology information
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMathews, I.I. / Soltis, M. / Saldajeno, M. / Ganshaw, G. / Sala, R. / Weyler, W. / Cervin, M.A. / Whited, G. / Bott, R.
CitationJournal: Biochemistry / Year: 2007
Title: Structure of a novel enzyme that catalyzes acyl transfer to alcohols in aqueous conditions.
Authors: Mathews, I. / Soltis, M. / Saldajeno, M. / Ganshaw, G. / Sala, R. / Weyler, W. / Cervin, M.A. / Whited, G. / Bott, R.
History
DepositionMay 22, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Aryl esterase
B: Aryl esterase
C: Aryl esterase
D: Aryl esterase
E: Aryl esterase
F: Aryl esterase
G: Aryl esterase
H: Aryl esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,6629
Polymers187,5668
Non-polymers961
Water38,4442134
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21111.1 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.754, 80.096, 85.974
Angle α, β, γ (deg.)104.10, 112.10, 97.40
Int Tables number1
Space group name H-MP1
DetailsThe bilogical assembly is an octamer. The coordinate files contains a biological octamer.

-
Components

#1: Protein
Aryl esterase


Mass: 23445.795 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC19686 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / References: UniProt: A0R5U7, arylesterase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2134 / 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: 2.17 Å3/Da / Density % sol: 43.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100mM Tris (pH 8.0), 2M ammonium sulfate, 2% PEG 400., VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 30, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 240647 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.042 / Rsym value: 0.042 / Net I/σ(I): 30.8
Reflection shellHighest resolution: 1.5 Å

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Native enzyme

Resolution: 1.5→50 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.96 / SU B: 0.795 / SU ML: 0.031 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.063 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15977 11930 5 %RANDOM
Rwork0.13414 ---
obs0.1354 228596 95.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 10.475 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20.53 Å20.45 Å2
2--0.35 Å20.59 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13144 0 5 2134 15283
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02213476
X-RAY DIFFRACTIONr_bond_other_d0.0010.0212528
X-RAY DIFFRACTIONr_angle_refined_deg1.6271.98218438
X-RAY DIFFRACTIONr_angle_other_deg0.904329056
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6151712
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.76623.788528
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.74152016
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7861580
X-RAY DIFFRACTIONr_chiral_restr0.1090.22144
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214984
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022632
X-RAY DIFFRACTIONr_nbd_refined0.2290.22653
X-RAY DIFFRACTIONr_nbd_other0.1830.212775
X-RAY DIFFRACTIONr_nbtor_refined0.1820.26942
X-RAY DIFFRACTIONr_nbtor_other0.0850.27288
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1140.21279
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2680.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1380.247
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1321.510949
X-RAY DIFFRACTIONr_mcbond_other0.2551.53464
X-RAY DIFFRACTIONr_mcangle_it1.312213936
X-RAY DIFFRACTIONr_scbond_it2.27335620
X-RAY DIFFRACTIONr_scangle_it3.3444.54502
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.164 906 -
Rwork0.111 16754 -
obs--94.59 %
Refinement TLS params.

L11: 0 °2 / L12: 0 °2 / L13: 0 °2 / L22: 0 °2 / L23: 0 °2 / L33: 0 °2 / S11: 0 Å ° / S12: 0 Å ° / S13: 0 Å ° / S21: 0 Å ° / S22: 0 Å ° / S23: 0 Å ° / S31: 0 Å ° / S32: 0 Å ° / S33: 0 Å ° / T11: 0 Å2 / T12: 0 Å2 / T13: 0 Å2 / T22: 0 Å2 / T23: 0 Å2 / T33: 0 Å2 / Method: refined / Origin x: 0 Å / Origin y: 0 Å / Origin z: 0 Å / Refine-ID: X-RAY DIFFRACTION

ID
1
2
3
4
5
6
7
8
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 2162 - 216
2X-RAY DIFFRACTION2BB2 - 2162 - 216
3X-RAY DIFFRACTION3CC2 - 2162 - 216
4X-RAY DIFFRACTION4DD2 - 2162 - 216
5X-RAY DIFFRACTION5EE2 - 2162 - 216
6X-RAY DIFFRACTION6FF2 - 2162 - 216
7X-RAY DIFFRACTION7GG2 - 2162 - 216
8X-RAY DIFFRACTION8HH2 - 2162 - 216

+
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