[English] 日本語
Yorodumi
- PDB-4qkr: Crystal Structure of 6xTyr/PV2: de novo designed beta-trefoil arc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4qkr
TitleCrystal Structure of 6xTyr/PV2: de novo designed beta-trefoil architecture with symmetric primary structure (L22Y/L44Y/L64Y/L85Y/L108Y/L132Y, Primitive Version 2)
ComponentsDE NOVO PROTEIN 6XTYR/PV2
KeywordsDE NOVO PROTEIN / simplified protein design / prebiotic protein / beta-trefoil
Function / homologyTrefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta / IMIDAZOLE
Function and homology information
Biological speciesSynthetic (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.746 Å
AuthorsLongo, L.M. / Blaber, M. / Tenorio, C.A.
CitationJournal: Protein Sci. / Year: 2015
Title: A single aromatic core mutation converts a designed "primitive" protein from halophile to mesophile folding.
Authors: Longo, L.M. / Tenorio, C.A. / Kumru, O.S. / Middaugh, C.R. / Blaber, M.
History
DepositionJun 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: DE NOVO PROTEIN 6XTYR/PV2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6922
Polymers14,6231
Non-polymers691
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.763, 46.792, 67.648
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein DE NOVO PROTEIN 6XTYR/PV2


Mass: 14622.649 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synthetic (others)
Description: Synthetic sequence derived from human acidic fibroblast growth factor with symmetric deconstruction method and enriched for pre-biotic amino acids.
Plasmid: pET21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 1.88 Å3/Da / Density % sol: 34.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 30% PEG 8,000, 0.1 M Imidazole HCl, 0.2 M NaCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.541 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 20, 2013
RadiationMonochromator: multi-layer mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 1.746→40 Å / Num. obs: 11690 / % possible obs: 99.6 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.052 / Χ2: 1.883 / Net I/σ(I): 18.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.75-1.815.90.31111120.632198.3
1.81-1.897.10.22311410.797199.5
1.89-1.977.50.17111411.038199.6
1.97-2.077.60.12311621.221199.7
2.07-2.27.60.09711421.353199.8
2.2-2.387.40.07811641.737199.9
2.38-2.617.60.06811702.0431100
2.61-2.997.60.05311712.2531100
2.99-3.777.50.04212032.756199.7
3.77-407.10.03712844.396199.8

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.746→33.824 Å / FOM work R set: 0.8463 / SU ML: 0.22 / σ(F): 1.37 / Phase error: 21.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2155 583 5 %Random
Rwork0.1866 ---
obs0.188 11651 99.4 %-
Solvent computationShrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.828 Å2 / ksol: 0.366 e/Å3
Displacement parametersBiso max: 80.55 Å2 / Biso mean: 26.29 Å2 / Biso min: 13.22 Å2
Baniso -1Baniso -2Baniso -3
1--0.4553 Å2-0 Å20 Å2
2---5.2079 Å2-0 Å2
3---5.6632 Å2
Refinement stepCycle: LAST / Resolution: 1.746→33.824 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms973 0 5 116 1094
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071053
X-RAY DIFFRACTIONf_angle_d1.1011441
X-RAY DIFFRACTIONf_chiral_restr0.074154
X-RAY DIFFRACTIONf_plane_restr0.006204
X-RAY DIFFRACTIONf_dihedral_angle_d15.06427
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7461-1.92180.29941400.25962673281398
1.9218-2.19980.25911440.19527212865100
2.1998-2.77130.23561460.192727762922100
2.7713-33.83030.17991530.171228983051100

+
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