[English] 日本語
Yorodumi
- PDB-6tbd: Crystal structure of the SVS_A2 protein from ancestral sequence r... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6tbd
TitleCrystal structure of the SVS_A2 protein from ancestral sequence reconstruction at 2.30 A resolution
ComponentsDesign protein SVS_A2
KeywordsBIOSYNTHETIC PROTEIN / Crystal structure of the design-protein SVS_A2 at 2.3 A resolution
Biological speciesStreptomyces sp. CWA1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsRudraraju, R. / Schnell, R. / Schneider, G.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council Sweden
CitationJournal: J.Am.Chem.Soc. / Year: 2021
Title: Engineering of Ancestors as a Tool to Elucidate Structure, Mechanism, and Specificity of Extant Terpene Cyclase.
Authors: Schriever, K. / Saenz-Mendez, P. / Rudraraju, R.S. / Hendrikse, N.M. / Hudson, E.P. / Biundo, A. / Schnell, R. / Syren, P.O.
History
DepositionNov 1, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 31, 2021Group: 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 1.3Jan 24, 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: Design protein SVS_A2
B: Design protein SVS_A2


Theoretical massNumber of molelcules
Total (without water)80,8172
Polymers80,8172
Non-polymers00
Water4,936274
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, The biologically relevant dimer is formed by A and B chains, as it is present in the asymmetric unit of the crystal
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-15 kcal/mol
Surface area24160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.300, 105.481, 105.481
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Design protein SVS_A2


Mass: 40408.711 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Artificial protein designed based on natural proteins form the terpene cyclase family
Source: (gene. exp.) Streptomyces sp. CWA1 (bacteria) / Gene: artificial design / Production host: Escherichia coli (E. coli) / References: EC: 4.2.3.158
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 2.62 Å3/Da / Density % sol: 53.05 % / Description: Rod
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M BTP pH 6.5 0.2 M Na-Phosphate 20% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 6, 2018 / Details: toroidal mirrors
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 2.3→43.2 Å / Num. obs: 37596 / % possible obs: 99.1 % / Observed criterion σ(I): 2.9 / Redundancy: 5.2 % / Biso Wilson estimate: 40.3 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.101 / Rrim(I) all: 0.172 / Net I/σ(I): 9
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.677 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 3635 / CC1/2: 0.758 / Rpim(I) all: 0.496 / Rrim(I) all: 0.853 / % possible all: 99.3

-
Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OKZ

4okz


Resolution: 2.3→43.2 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.935 / SU B: 6.624 / SU ML: 0.156 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.268 / ESU R Free: 0.199
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.218 1913 5.1 %RANDOM
Rwork0.1838 ---
obs0.1856 35565 98.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 127.23 Å2 / Biso mean: 35.81 Å2 / Biso min: 13.04 Å2
Baniso -1Baniso -2Baniso -3
1-1.46 Å20 Å2-0 Å2
2---1.17 Å20 Å2
3----0.29 Å2
Refinement stepCycle: final / Resolution: 2.3→43.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5084 0 0 274 5358
Biso mean---34.03 -
Num. residues----643
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0195247
X-RAY DIFFRACTIONr_bond_other_d0.0020.024898
X-RAY DIFFRACTIONr_angle_refined_deg1.581.9347135
X-RAY DIFFRACTIONr_angle_other_deg1.028311192
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1015642
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.23321.901263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.00615809
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4921566
X-RAY DIFFRACTIONr_chiral_restr0.0950.2752
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215995
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021321
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 134 -
Rwork0.246 2607 -
all-2741 -
obs--98.56 %

+
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