[English] 日本語
Yorodumi
- PDB-3s0r: Crystal Structure of De novo Designed helical assembly protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3s0r
TitleCrystal Structure of De novo Designed helical assembly protein
ComponentsDe novo designed Helical Assembly
KeywordsDE NOVO PROTEIN / Interacts with Single Walled Nanotube (SWNT)
Biological speciesartificial gene (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.453 Å
AuthorsAcharya, R. / Grigoryan, G. / Kim, Y.H. / DeGrado, W.F.
CitationJournal: Science / Year: 2011
Title: Computational design of virus-like protein assemblies on carbon nanotube surfaces.
Authors: Grigoryan, G. / Kim, Y.H. / Acharya, R. / Axelrod, K. / Jain, R.M. / Willis, L. / Drndic, M. / Kikkawa, J.M. / DeGrado, W.F.
History
DepositionMay 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 17, 2011Group: Source and taxonomy
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: De novo designed Helical Assembly
B: De novo designed Helical Assembly


Theoretical massNumber of molelcules
Total (without water)6,3772
Polymers6,3772
Non-polymers00
Water32418
1
A: De novo designed Helical Assembly
B: De novo designed Helical Assembly

A: De novo designed Helical Assembly
B: De novo designed Helical Assembly


Theoretical massNumber of molelcules
Total (without water)12,7544
Polymers12,7544
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_655-x+1,-y,z1
Buried area5020 Å2
ΔGint-47 kcal/mol
Surface area6790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.529, 45.529, 93.293
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

-
Components

#1: Protein/peptide De novo designed Helical Assembly / HexCoil-Ala helical Assembly


Mass: 3188.565 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) artificial gene (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 3.79 Å3/Da / Density % sol: 67.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: The 2 uL drop consisted of a 1:1 v/v mixture of 5 mg/mL protein solution (in 20 mM sodium phosphate, pH 7.5, 100 mM NaCl) and reservoir solution (75 mM HEPES sodium, pH 7.5, 0.6 M sodium ...Details: The 2 uL drop consisted of a 1:1 v/v mixture of 5 mg/mL protein solution (in 20 mM sodium phosphate, pH 7.5, 100 mM NaCl) and reservoir solution (75 mM HEPES sodium, pH 7.5, 0.6 M sodium phosphate monobasic monohydrate, 0.6 M potassium phosphate monobasic, 25% v/v glycerol) , VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: May 21, 2010 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.499
ReflectionResolution: 2.44→18.888 Å / Num. all: 3501 / Num. obs: 3479 / % possible obs: 89.5 % / Observed criterion σ(I): 3 / Redundancy: 7.4 % / Biso Wilson estimate: 38.2 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 20.5
Reflection shellResolution: 2.44→2.57 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.168 / Mean I/σ(I) obs: 10.8 / Num. unique all: 434 / % possible all: 81.8

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 30-residue polyalanine alpha helix

Resolution: 2.453→18.888 Å / Cross valid method: THROUGHOUT / σ(F): 2.07 / Phase error: 30.11 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2752 314 9.03 %RANDOM
Rwork0.2472 ---
obs0.2529 3479 99.63 %-
all-3492 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 78.95 Å2 / ksol: 0.5 e/Å3
Displacement parametersBiso mean: 28.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.2633 Å20 Å2-0 Å2
2--2.2633 Å2-0 Å2
3----4.5266 Å2
Refinement stepCycle: LAST / Resolution: 2.453→18.888 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms446 0 0 18 464
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007446
X-RAY DIFFRACTIONf_angle_d1.155598
X-RAY DIFFRACTIONf_dihedral_angle_d20.094164
X-RAY DIFFRACTIONf_chiral_restr0.05970
X-RAY DIFFRACTIONf_plane_restr0.00380
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2 / % reflection obs: 91 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.4572-3.090.26761580.25941556
3.09-13.75640.28591560.2431585

+
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