[English] 日本語
Yorodumi
- PDB-6vap: Structure of the type II thioesterase BorB from the borrelidin bi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6vap
TitleStructure of the type II thioesterase BorB from the borrelidin biosynthetic cluster
ComponentsThioesterase
KeywordsBIOSYNTHETIC PROTEIN / thioesterase
Function / homology
Function and homology information


lipid biosynthetic process / hydrolase activity
Similarity search - Function
Thioesterase type II, NRPS/PKS/S-FAS / Polyketide synthase, thioesterase domain / Thioesterase / Thioesterase / Thioesterase domain / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesStreptomyces sp. WAC02707 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsPereira, J.H. / Curran, S.C. / Baluyot, M.-J. / Lake, J. / Putz, H. / Rosenburg, D. / Keasling, J. / Adams, P.D.
CitationJournal: Biochemistry / Year: 2020
Title: Structure and Function of BorB, the Type II Thioesterase from the Borrelidin Biosynthetic Gene Cluster.
Authors: Curran, S.C. / Pereira, J.H. / Baluyot, M.J. / Lake, J. / Puetz, H. / Rosenburg, D.J. / Adams, P. / Keasling, J.D.
History
DepositionDec 17, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1May 13, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 2023Group: 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: Thioesterase
B: Thioesterase


Theoretical massNumber of molelcules
Total (without water)58,7742
Polymers58,7742
Non-polymers00
Water6,593366
1
A: Thioesterase


Theoretical massNumber of molelcules
Total (without water)29,3871
Polymers29,3871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Thioesterase


Theoretical massNumber of molelcules
Total (without water)29,3871
Polymers29,3871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.450, 92.360, 150.140
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11B-338-

HOH

21B-377-

HOH

-
Components

#1: Protein Thioesterase


Mass: 29387.199 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. WAC02707 (bacteria) / Gene: EF919_13485 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A454WD44
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / 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: 2.14 Å3/Da / Density % sol: 42.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Magnesium Chloride, 0.1 M Hepes pH 7.5, 22% Poly (acrylic acid sodium salt) 5100

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.89→46.23 Å / Num. obs: 39997 / % possible obs: 95.3 % / Redundancy: 8 % / Biso Wilson estimate: 27.26 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.143 / Net I/σ(I): 10.07
Reflection shellResolution: 1.89→1.96 Å / Num. unique obs: 3844 / CC1/2: 0.874

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FLA

3fla


Resolution: 1.93→46.18 Å / SU ML: 0.3022 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.3122
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2497 1883 4.96 %
Rwork0.2093 36055 -
obs0.2113 37938 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.68 Å2
Refinement stepCycle: LAST / Resolution: 1.93→46.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3747 0 0 366 4113
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113846
X-RAY DIFFRACTIONf_angle_d0.98335240
X-RAY DIFFRACTIONf_chiral_restr0.055575
X-RAY DIFFRACTIONf_plane_restr0.0076698
X-RAY DIFFRACTIONf_dihedral_angle_d19.77661419
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.980.45141440.39232720X-RAY DIFFRACTION98.83
1.98-2.040.33821470.27242733X-RAY DIFFRACTION99.11
2.04-2.110.27571360.25352765X-RAY DIFFRACTION99.25
2.11-2.180.29561470.23662737X-RAY DIFFRACTION99.24
2.18-2.270.48581450.42172656X-RAY DIFFRACTION95.83
2.27-2.370.3021450.2252737X-RAY DIFFRACTION99.41
2.37-2.50.22011380.20042762X-RAY DIFFRACTION99.59
2.5-2.650.22621260.19672805X-RAY DIFFRACTION99.73
2.65-2.860.25251700.2042742X-RAY DIFFRACTION99.69
2.86-3.150.21751420.19332805X-RAY DIFFRACTION99.9
3.15-3.60.23941350.17742824X-RAY DIFFRACTION99.76
3.6-4.540.18421590.16492830X-RAY DIFFRACTION99.63
4.54-46.180.21621490.17912939X-RAY DIFFRACTION99.71

+
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