[English] 日本語
Yorodumi
- PDB-4w5y: Crystal structure of Prp pepttide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4w5y
TitleCrystal structure of Prp pepttide
ComponentsPrp peptide
Keywordsde novo protein / membrane protein / prion peptide
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.122 Å
AuthorsYu, L. / Lee, S.-J. / Yee, V.
CitationJournal: Biochemistry / Year: 2015
Title: Crystal Structures of Polymorphic Prion Protein beta 1 Peptides Reveal Variable Steric Zipper Conformations.
Authors: Yu, L. / Lee, S.J. / Yee, V.C.
History
DepositionAug 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2015Group: Derived calculations
Revision 1.2Jul 1, 2015Group: Database references
Revision 1.3Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Refinement description / Source and taxonomy
Category: citation / pdbx_entity_src_syn ...citation / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_entity_src_syn.pdbx_alt_source_flag ..._citation.journal_id_CSD / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Prp peptide
B: Prp peptide


Theoretical massNumber of molelcules
Total (without water)1,3962
Polymers1,3962
Non-polymers00
Water1629
1
A: Prp peptide

A: Prp peptide

A: Prp peptide

A: Prp peptide

B: Prp peptide

B: Prp peptide

B: Prp peptide

B: Prp peptide


Theoretical massNumber of molelcules
Total (without water)5,5828
Polymers5,5828
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
crystal symmetry operation1_655x+1,y,z2
crystal symmetry operation1_665x+1,y+1,z1
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation1_545x,y-1,z1
crystal symmetry operation1_645x+1,y-1,z1
Unit cell
Length a, b, c (Å)9.467, 10.439, 21.985
Angle α, β, γ (deg.)79.750, 81.890, 66.750
Int Tables number1
Space group name H-MP1
DetailsBIOLOGICAL UNIT DISPLAYS ONLY A PORTION OF THE CRYSTAL LATTICE TO DEMONSTRATE THE CRYSTAL PACKING CONTENT. THE CRYSTAL PACKING IS FORMED BY A REPETITION IN BOTH DIRECTIONS OF THE PORTION INDICATED IN REMARK 350.

-
Components

#1: Protein/peptide Prp peptide


Mass: 697.802 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 1.4 Å3/Da / Density % sol: 12.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Hepes, 2.0 M ammonium sulfate, and 2.0 M NDSB-211

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9184 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 14, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.12→50 Å / Num. obs: 2879 / % possible obs: 98.4 % / Redundancy: 10 % / Biso Wilson estimate: 1.89 Å2 / Rmerge(I) obs: 0.056 / Χ2: 1 / Net I/av σ(I): 41.126 / Net I/σ(I): 17.2 / Num. measured all: 28915
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.12-1.166.90.0832730.97590.7
1.16-1.219.60.0882951.00398.3
1.21-1.26100.0882781.00598.9
1.26-1.339.40.072931.00999.3
1.33-1.4110.10.077281199.6
1.41-1.5210.40.0623011100
1.52-1.67110.0622840.99699.3
1.67-1.9210.80.0513010.991100
1.92-2.4111.40.0442891.00799.7
2.41-5010.70.042841.00898.3

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
PDB_EXTRACT3.15data extraction
SHELXphasing
PHENIX(phenix.refine: 1.9_1692)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.122→10.784 Å / SU ML: 0 / Cross valid method: FREE R-VALUE / σ(F): 2.21 / Phase error: 10.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1 130 4.52 %
Rwork0.0812 2744 -
obs0.0822 2874 98.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 8.99 Å2 / Biso mean: 2.7084 Å2 / Biso min: 0.93 Å2
Refinement stepCycle: final / Resolution: 1.122→10.784 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms96 0 0 9 105
Biso mean---7.03 -
Num. residues----14
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009102
X-RAY DIFFRACTIONf_angle_d1.259135
X-RAY DIFFRACTIONf_chiral_restr0.05313
X-RAY DIFFRACTIONf_plane_restr0.00417
X-RAY DIFFRACTIONf_dihedral_angle_d12.23737
LS refinement shellResolution: 1.1224→10.7844 Å / Total num. of bins used: 1
RfactorNum. reflection% reflection
Rfree0.1 130 -
Rwork0.0812 2744 -
all-2874 -
obs--99 %

+
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://pdbjlvh1.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