[English] 日本語
Yorodumi
- PDB-4olr: [Leu-5]-Enkephalin mutant - YVVFV -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4olr
Title[Leu-5]-Enkephalin mutant - YVVFV
Components[Leu-5]-Enkephalin mutant - YVVFV
KeywordsPROTEIN FIBRIL / amyloid-like protofibril
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.1 Å
AuthorsSangwan, S. / Eisenberg, D. / Sawaya, M.R. / Do, T.D. / Bowers, M.T. / Lapointe, N.E. / Teplow, D.B. / Feinstein, S.C.
CitationJournal: J.Phys.Chem.B / Year: 2014
Title: Factors that drive Peptide assembly from native to amyloid structures: experimental and theoretical analysis of [leu-5]-enkephalin mutants.
Authors: Do, T.D. / LaPointe, N.E. / Sangwan, S. / Teplow, D.B. / Feinstein, S.C. / Sawaya, M.R. / Eisenberg, D.S. / Bowers, M.T.
History
DepositionJan 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2014Group: Database references
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: [Leu-5]-Enkephalin mutant - YVVFV
B: [Leu-5]-Enkephalin mutant - YVVFV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,3703
Polymers1,2522
Non-polymers1181
Water905
1
A: [Leu-5]-Enkephalin mutant - YVVFV
B: [Leu-5]-Enkephalin mutant - YVVFV
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)8,21818
Polymers7,50912
Non-polymers7096
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation1_755x+2,y,z1
crystal symmetry operation2_555-x,y+1/2,-z1
crystal symmetry operation2_655-x+1,y+1/2,-z1
crystal symmetry operation2_755-x+2,y+1/2,-z1
Unit cell
Length a, b, c (Å)9.750, 21.380, 19.050
Angle α, β, γ (deg.)90.000, 93.170, 90.000
Int Tables number4
Space group name H-MP1211
Details;The biological unit is a pair of beta sheets. One sheet is constructed from chains A and B with unit cell translations along the a direction (i.e. X+1,Y,Z; X+2,Y,Z; X+3,Y,Z, etc.). The second sheet is constructed from -X,1/2+Y,-Z; 1-X,1/2+Y,-Z; 2-X,1/2+Y,-Z; etc.)

-
Components

#1: Protein/peptide [Leu-5]-Enkephalin mutant - YVVFV


Mass: 625.755 Da / Num. of mol.: 2 / Fragment: [Leu-5]-Enkephalin / Mutation: G2V,G3V,L5V / Source method: obtained synthetically / Details: synthesized / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 1.58 Å3/Da / Density % sol: 22.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: reservoir contained 15% MPD, 0.1M Sodium Cacodylate, 0.1M Magnesium Acetate, pH 6.5, vapor diffusion, hanging drop, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.1→19.02 Å / Num. all: 3191 / Num. obs: 3191 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 6.65 % / Biso Wilson estimate: 5.6 Å2 / Rmerge(I) obs: 0.212 / Net I/σ(I): 5.91
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.1-1.130.7691.590120390.2
1.13-1.160.9741.7138823297.5
1.16-1.190.8672.15150521997.3
1.19-1.230.9042152622498.7
1.23-1.270.6862.62140020097.6
1.27-1.320.5593.07135819799
1.32-1.360.4683.72143220998.6
1.36-1.420.4593.97125518299.5
1.42-1.480.4054.51125218299.5
1.48-1.560.2726.05125618199.5
1.56-1.640.236.651142164100
1.64-1.740.2097.391086155100
1.74-1.860.1759.11021147100
1.86-2.010.14610.961011148100
2.01-2.20.11712.15836122100
2.2-2.460.09612.72808124100
2.46-2.840.11113.6466898100
2.84-3.480.114.7665793100
3.48-4.920.09916.25067398.6
4.920.09514.082363897.4

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.14data extraction
SHELXDphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.1→19.02 Å / FOM work R set: 0.8699 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 19.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1871 316 9.97 %Random
Rwork0.1497 ---
all0.1532 3170 --
obs0.1532 3170 98.05 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 31.87 Å2 / Biso mean: 8.36 Å2 / Biso min: 3.71 Å2
Refinement stepCycle: LAST / Resolution: 1.1→19.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms90 0 8 5 103
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0199
X-RAY DIFFRACTIONf_angle_d1.376136
X-RAY DIFFRACTIONf_chiral_restr0.10417
X-RAY DIFFRACTIONf_plane_restr0.00514
X-RAY DIFFRACTIONf_dihedral_angle_d10.53128
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.1002-1.38610.27231550.22771397155297
1.3861-19.02380.14511610.11414571618100

+
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