[English] 日本語
Yorodumi
- PDB-1byz: DESIGNED PEPTIDE ALPHA-1, P1 FORM -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1byz
TitleDESIGNED PEPTIDE ALPHA-1, P1 FORM
ComponentsPROTEIN (SYNTHETIC DESIGNED PEPTIDE "ALPHA-1")
KeywordsDE NOVO PROTEIN / HELICAL BILAYER / BIOMATERIAL
Function / homologyETHANOLAMINE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIRECT METHODS / Resolution: 0.9 Å
AuthorsPrive, G.G. / Anderson, D.H. / Wesson, L. / Cascio, D. / Eisenberg, D.
Citation
Journal: Protein Sci. / Year: 1999
Title: Packed protein bilayers in the 0.90 A resolution structure of a designed alpha helical bundle.
Authors: Prive, G.G. / Anderson, D.H. / Wesson, L. / Cascio, D. / Eisenberg, D.
#1: Journal: Protein Sci. / Year: 1999
Title: Centrosymmetric Bilayers in the 0.75A Resolution Structure of a Designed Alpha- Helical Peptide, D, L-Alpha-1
Authors: Patterson, W.R. / Anderson, D.H. / Degrado, W.F. / Cascio, D. / Eisenberg, D.
#2: Journal: Science / Year: 1990
Title: Crystal Structure of Alpha-1: Implications for Protein Design
Authors: Hill, C.P. / Anderson, D.H. / Wesson, L. / Degrado, W.F. / Eisenberg, D.
#3: Journal: Proteins / Year: 1986
Title: The Design, Synthesis, and Crystallization of an Alpha-Helical Peptide
Authors: Eisenberg, D. / Wilcox, W. / Eshita, S.M. / Pryciak, P.M. / Ho, S.P. / De Grado, W.F.
History
DepositionOct 20, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 28, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4May 30, 2018Group: Data collection / Experimental preparation ...Data collection / Experimental preparation / Source and taxonomy / Structure summary
Category: entity / exptl_crystal / pdbx_entity_src_syn
Item: _entity.src_method / _exptl_crystal.density_Matthews / _exptl_crystal.density_percent_sol
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (SYNTHETIC DESIGNED PEPTIDE "ALPHA-1")
B: PROTEIN (SYNTHETIC DESIGNED PEPTIDE "ALPHA-1")
C: PROTEIN (SYNTHETIC DESIGNED PEPTIDE "ALPHA-1")
D: PROTEIN (SYNTHETIC DESIGNED PEPTIDE "ALPHA-1")
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,39711
Polymers5,7674
Non-polymers6307
Water54030
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)20.846, 20.909, 27.057
Angle α, β, γ (deg.)102.40, 95.33, 119.62
Int Tables number1
Space group name H-MP1

-
Components

-
Protein/peptide , 1 types, 4 molecules ABCD

#1: Protein/peptide
PROTEIN (SYNTHETIC DESIGNED PEPTIDE "ALPHA-1")


Mass: 1441.775 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: N TERMINI ARE ACETYLATED / Source: (synth.) synthetic construct (others)

-
Non-polymers , 5 types, 37 molecules

#2: Chemical ChemComp-ETA / ETHANOLAMINE / Ethanolamine


Type: L-peptide COOH carboxy terminus / Mass: 61.083 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H7NO
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


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


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O

-
Details

Nonpolymer detailsMPD 513 IS BUILT IN TWO OVERLAPPING CONFORMATIONS. ALL THE WATERS ARE IN SINGLE SITES.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.69 Å3/Da / Density % sol: 27.13 % / Description: SNB SUCCESS RATE WAS 5%.
Crystal growMethod: vapor diffusion, sitting drop / pH: 8
Details: 91% 2-METHYL-2,4-PENTANEDIOL, 78mM TRIETHANOLAMINE-HCL pH8, 52mM ETHANOLAMINE-HCL pH9.75, pH 8.0, VAPOR DIFFUSION, SITTING DROP
Crystal grow
*PLUS
Details: drop consists of equal volume of peptide and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlpeptide1drop
278 mMtriethanolamine-HCl1reservoir
352 mMethanolamine-HCl1reservoir
491 %MPD1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 15, 1994
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 0.9→25.7 Å / Num. obs: 23681 / % possible obs: 85.9 % / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Rsym value: 0.076 / Net I/σ(I): 16.3
Reflection shellResolution: 0.9→0.93 Å / Redundancy: 1.3 % / Mean I/σ(I) obs: 4.3 / Rsym value: 0.141 / % possible all: 36
Reflection
*PLUS
Highest resolution: 0.9 Å / Lowest resolution: 25.7 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.076
Reflection shell
*PLUS
% possible obs: 36 % / Num. unique obs: 1011 / Rmerge(I) obs: 0.141 / Mean I/σ(I) obs: 4.3

-
Processing

Software
NameVersionClassification
SHAKEmodel building
SnB(SNB 1.5) MILLERphasing
SHELXLrefinement
SHELXL-97refinement
DENZO(DENZO)data reduction
SCALEPACK(DENZO)data scaling
RefinementMethod to determine structure: DIRECT METHODS
Starting model: 448 RANDOM ATOMS

Resolution: 0.9→25.7 Å / Num. parameters: 4695 / Num. restraintsaints: 5898 / Cross valid method: FREE R / σ(F): 2
StereochEM target val spec case: ETHANOLAMINE AND MPD RESTRAINTS WERE DERIVED BY ANALOGY TO OTHER SIMILAR GROUPS
Stereochemistry target values: ENGH AND HUBER
Details: MORE LOW-OCCUPANCY DISCRETE DISORDER COULD BE BUILT FOR SOLVENT AND PEPTIDE, BUT WOULD EXCESSIVELY INCREASE THE NUMBER OF REFINEABLE PARAMETERS.
RfactorNum. reflection% reflectionSelection details
Rfree0.105 2368 10 %EVERY TENTH REFLECTION SAME TEST SET FOR SHELXL-93 AND SHELXL-97
all0.086 23681 --
obs0.085 -85.9 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2
Refine analyzeNum. disordered residues: 7 / Occupancy sum hydrogen: 544 / Occupancy sum non hydrogen: 478.97
Refinement stepCycle: LAST / Resolution: 0.9→25.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms408 0 41 30 479
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.025
X-RAY DIFFRACTIONs_angle_d0
X-RAY DIFFRACTIONs_similar_dist0.016
X-RAY DIFFRACTIONs_from_restr_planes0.017
X-RAY DIFFRACTIONs_zero_chiral_vol0.065
X-RAY DIFFRACTIONs_non_zero_chiral_vol0
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.192
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.026
X-RAY DIFFRACTIONs_approx_iso_adps0.108
Software
*PLUS
Name: SHELXL / Version: 93 and 97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 0.9 Å / Rfactor obs: 0.086
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONs_bond_d0.03
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg0.061.9
X-RAY DIFFRACTIONs_chiral_restr0.20.065
LS refinement shell
*PLUS
Highest resolution: 0.9 Å / Lowest resolution: 1.01 Å / Rfactor Rwork: 0.164

+
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