[English] 日本語
Yorodumi
- PDB-3rli: Crystal structure of monoacylglycerol lipase from Bacillus sp. H2... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3rli
TitleCrystal structure of monoacylglycerol lipase from Bacillus sp. H257 in complex with PMSF
ComponentsThermostable monoacylglycerol lipase
KeywordsHYDROLASE / alpha/beta hydrolase
Function / homology
Function and homology information


acylglycerol lipase / monoacylglycerol lipase activity / carboxylic ester hydrolase activity
Similarity search - Function
Esterase/lipase / : / Serine aminopeptidase, S33 / Serine aminopeptidase, S33 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
phenylmethanesulfonic acid / Thermostable monoacylglycerol lipase
Similarity search - Component
Biological speciesBacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.854 Å
AuthorsRengachari, S. / Bezerra, G.A. / Gruber, K. / Oberer, M.
CitationJournal: Biochim.Biophys.Acta / Year: 2012
Title: The structure of monoacylglycerol lipase from Bacillus sp. H257 reveals unexpected conservation of the cap architecture between bacterial and human enzymes.
Authors: Rengachari, S. / Bezerra, G.A. / Riegler-Berket, L. / Gruber, C.C. / Sturm, C. / Taschler, U. / Boeszoermenyi, A. / Dreveny, I. / Zimmermann, R. / Gruber, K. / Oberer, M.
History
DepositionApr 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: 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 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Thermostable monoacylglycerol lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8513
Polymers29,5611
Non-polymers2902
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.050, 70.690, 43.440
Angle α, β, γ (deg.)90.000, 111.650, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Thermostable monoacylglycerol lipase / MGLP


Mass: 29560.611 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. (bacteria) / Strain: H257 / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P82597, acylglycerol lipase
#2: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-PMS / phenylmethanesulfonic acid


Mass: 172.202 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8O3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 1.84 Å3/Da / Density % sol: 33.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES/imidazole pH 6.5, 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, and 0.02 M of monosaccharides (D-glucose, D-mannose, D-galactose, L-fuctose, D-xylose, and N-acetyl-D- ...Details: 0.1 M MES/imidazole pH 6.5, 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, and 0.02 M of monosaccharides (D-glucose, D-mannose, D-galactose, L-fuctose, D-xylose, and N-acetyl-D-glucosamine), VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.81 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 31, 2010
RadiationMonochromator: Si 111, horizontally focussing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81 Å / Relative weight: 1
ReflectionResolution: 1.854→40.376 Å / Num. all: 17878 / Num. obs: 17878 / % possible obs: 96.2 % / Redundancy: 3.1 % / Biso Wilson estimate: 15.56 Å2 / Rsym value: 0.057
Reflection shellResolution: 1.854→1.94 Å / % possible all: 96.2

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 27.63
Highest resolutionLowest resolution
Rotation2.5 Å26.59 Å
Translation2.5 Å26.59 Å

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.9data scaling
PHASERphasing
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RM3

3rm3


Resolution: 1.854→17.683 Å / Occupancy max: 1 / Occupancy min: 0.46 / FOM work R set: 0.8828 / SU ML: 0.21 / σ(F): 0 / Phase error: 18.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1939 889 5.06 %
Rwork0.156 --
obs0.1579 17561 96.6 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.738 Å2 / ksol: 0.437 e/Å3
Displacement parametersBiso max: 71.65 Å2 / Biso mean: 17.4197 Å2 / Biso min: 4.06 Å2
Baniso -1Baniso -2Baniso -3
1-0.6174 Å20 Å2-0.3725 Å2
2--0.1538 Å20 Å2
3----0.7713 Å2
Refinement stepCycle: LAST / Resolution: 1.854→17.683 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1884 0 18 202 2104
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131971
X-RAY DIFFRACTIONf_angle_d1.0512685
X-RAY DIFFRACTIONf_chiral_restr0.066300
X-RAY DIFFRACTIONf_plane_restr0.005347
X-RAY DIFFRACTIONf_dihedral_angle_d14.173720
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.854-1.97050.27211420.2142617275991
1.9705-2.12240.23171630.172778294197
2.1224-2.33560.21911460.15982799294598
2.3356-2.67260.21621420.15892837297998
2.6726-3.36330.17491640.14862821298598
3.3633-17.68370.15111320.13972820295296

+
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