[English] 日本語
Yorodumi
- PDB-1qys: Crystal structure of Top7: A computationally designed protein wit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qys
TitleCrystal structure of Top7: A computationally designed protein with a novel fold
ComponentsTOP7
KeywordsDE NOVO PROTEIN / alpha-beta / computationally designed / novel fold
Function / homologytop7, de novo designed protein / top7, de novo designed protein / 2-Layer Sandwich / Alpha Beta
Function and homology information
Biological speciesComputationally Designed Sequence
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsKuhlman, B. / Dantas, G. / Ireton, G.C. / Varani, G. / Stoddard, B.L. / Baker, D.
CitationJournal: Science / Year: 2003
Title: Design of a Novel Globular Protein Fold with Atomic-Level Accuracy
Authors: Kuhlman, B. / Dantas, G. / Ireton, G.C. / Varani, G. / Stoddard, B.L. / Baker, D.
History
DepositionSep 11, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TOP7


Theoretical massNumber of molelcules
Total (without water)12,1301
Polymers12,1301
Non-polymers00
Water1267
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.900, 35.900, 140.554
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein TOP7


Mass: 12130.249 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Computationally Designed Sequence / Plasmid: pet29b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.16 Å3/Da / Density % sol: 42.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop, streak seeding / pH: 6.6
Details: 15-20% PEG3350 250mM Ammonium Formate, pH 6.6, VAPOR DIFFUSION, HANGING DROP, STREAK SEEDING, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
125 mg/mlprotein1drop
215-20 %PEG33501reservoir
3250 mMammonium formate1reservoirpH6.6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 24, 2003
RadiationMonochromator: DOUBLE CRYSTAL Si(111) / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 6979 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 30.2 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 37.8
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 5 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 6989 / % possible obs: 99.1 % / Num. measured all: 144933
Reflection shell
*PLUS
% possible obs: 100 %

-
Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→18.71 Å / Rfactor Rfree error: 0.016 / Data cutoff high absF: 1873860.4 / Data cutoff high rms absF: 1873860.4 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.293 346 5.1 %RANDOM
Rwork0.268 ---
obs0.268 6736 96.1 %-
all-6736 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.2431 Å2 / ksol: 0.300247 e/Å3
Displacement parametersBiso mean: 65.5 Å2
Baniso -1Baniso -2Baniso -3
1-10.54 Å29.56 Å20 Å2
2--10.54 Å20 Å2
3----21.07 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 2.5→18.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms685 0 0 7 692
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d26.3
X-RAY DIFFRACTIONc_improper_angle_d0.73
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.055 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.37 45 4.3 %
Rwork0.353 1009 -
obs--91.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0076
X-RAY DIFFRACTIONc_angle_deg1.35
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.73

+
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