[English] 日本語
Yorodumi
- PDB-6fza: Crystal Structure of lipase from Geobacillus stearothermophilus T... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6fza
TitleCrystal Structure of lipase from Geobacillus stearothermophilus T6 methanol stable variant A187F
ComponentsLipase
KeywordsHYDROLASE / lipase / methanol / organic solvent
Function / homology
Function and homology information


triacylglycerol lipase / triacylglycerol lipase activity / lipid catabolic process / extracellular region / metal ion binding
Similarity search - Function
: / Lipase-like, C-terminal domain / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
triacylglycerol lipase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsGihaz, S. / Kanteev, M. / Pazy, Y. / Fishman, A.
CitationJournal: Appl.Environ.Microbiol. / Year: 2018
Title: Filling the Void: Introducing Aromatic Interactions into Solvent Tunnels To Enhance Lipase Stability in Methanol.
Authors: Gihaz, S. / Kanteev, M. / Pazy, Y. / Fishman, A.
History
DepositionMar 14, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.title / _citation_author.identifier_ORCID / _entity.formula_weight
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0283
Polymers43,9221
Non-polymers1052
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-12 kcal/mol
Surface area15420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.471, 71.260, 112.223
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Lipase


Mass: 43922.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q93A71, triacylglycerol lipase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 2.25 Å3/Da / Density % sol: 45.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2M sodium formate, 20% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.75→45.27 Å / Num. obs: 35332 / % possible obs: 86.6 % / Redundancy: 4.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Rrim(I) all: 0.054 / Net I/σ(I): 19.2
Reflection shellResolution: 1.75→1.8015 Å

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X6U

4x6u


Resolution: 1.75→38.21 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.1
RfactorNum. reflection% reflection
Rfree0.2311 1733 4.91 %
Rwork0.2161 --
obs0.2168 35290 86.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.75→38.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3107 0 2 205 3314
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.033198
X-RAY DIFFRACTIONf_angle_d1.7864348
X-RAY DIFFRACTIONf_dihedral_angle_d14.7381133
X-RAY DIFFRACTIONf_chiral_restr0.146450
X-RAY DIFFRACTIONf_plane_restr0.01571
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.80150.27791190.25422305X-RAY DIFFRACTION73
1.8015-1.85960.27821170.24742352X-RAY DIFFRACTION74
1.8596-1.92610.29741230.23152400X-RAY DIFFRACTION75
1.9261-2.00320.22981300.22312465X-RAY DIFFRACTION77
2.0032-2.09440.25541460.22452510X-RAY DIFFRACTION79
2.0944-2.20480.20381200.22152636X-RAY DIFFRACTION82
2.2048-2.34290.24861440.21862814X-RAY DIFFRACTION87
2.3429-2.52380.22851660.2223021X-RAY DIFFRACTION95
2.5238-2.77770.26331580.22383186X-RAY DIFFRACTION98
2.7777-3.17950.24091710.22183142X-RAY DIFFRACTION97
3.1795-4.00510.21071630.20353289X-RAY DIFFRACTION100
4.0051-38.2190.20711760.20343437X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -10.5707 Å / Origin y: 10.1834 Å / Origin z: -18.0661 Å
111213212223313233
T0.0926 Å2-0.0207 Å2-0.0061 Å2-0.0993 Å2-0.0021 Å2--0.0987 Å2
L0.5907 °2-0.1939 °20.1318 °2-0.9684 °20.0762 °2--0.5805 °2
S-0.0197 Å °-0.03 Å °-0.0039 Å °0.0186 Å °-0.0087 Å °-0.0174 Å °0.0175 Å °0.0158 Å °0.0232 Å °
Refinement TLS groupSelection details: all

+
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