[English] 日本語
Yorodumi
- PDB-1qsu: CRYSTAL STRUCTURE OF THE TRIPLE-HELICAL COLLAGEN-LIKE PEPTIDE, (P... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qsu
TitleCRYSTAL STRUCTURE OF THE TRIPLE-HELICAL COLLAGEN-LIKE PEPTIDE, (PRO-HYP-GLY)4-GLU-LYS-GLY(PRO-HYP-GLY)5
ComponentsPROTEIN ((PRO-HYP-GLY)4- GLU-LYS-GLY(PRO-HYP-GLY)5)
KeywordsSTRUCTURAL PROTEIN / TRIPLE HELIX
MethodX-RAY DIFFRACTION / Resolution: 1.75 Å
AuthorsKramer, R.Z. / Venugopal, M. / Bella, J. / Brodsky, B. / Berman, H.M.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Staggered molecular packing in crystals of a collagen-like peptide with a single charged pair.
Authors: Kramer, R.Z. / Venugopal, M.G. / Bella, J. / Mayville, P. / Brodsky, B. / Berman, H.M.
History
DepositionJun 23, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN ((PRO-HYP-GLY)4- GLU-LYS-GLY(PRO-HYP-GLY)5)
B: PROTEIN ((PRO-HYP-GLY)4- GLU-LYS-GLY(PRO-HYP-GLY)5)
C: PROTEIN ((PRO-HYP-GLY)4- GLU-LYS-GLY(PRO-HYP-GLY)5)


Theoretical massNumber of molelcules
Total (without water)8,2173
Polymers8,2173
Non-polymers00
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5350 Å2
ΔGint-26 kcal/mol
Surface area4900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.326, 26.573, 45.885
Angle α, β, γ (deg.)90.00, 96.04, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein/peptide PROTEIN ((PRO-HYP-GLY)4- GLU-LYS-GLY(PRO-HYP-GLY)5)


Mass: 2738.892 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: Collagen-like model sequence.
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.16 Å3/Da / Density % sol: 42.97 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4K, tris HCl, Li2SO4, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlpeptide1drop
215 %PEG40001drop
30.1 MTris-HCl1drop
40.3 M1dropLi2SO4
50.1 MTris1reservoir
60.6 M1reservoirLi2SO4
730 %PEG40001reservoir

-
Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS CAD4 / Detector: DIFFRACTOMETER / Date: Oct 15, 1993
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 1.75 Å / Num. all: 7286 / % possible obs: 99.97 % / Observed criterion σ(F): 0
Reflection shellResolution: 1.75→1.81 Å / Num. unique all: 718 / % possible all: 99.86
Reflection
*PLUS
Num. obs: 5745
Reflection shell
*PLUS
% possible obs: 99.9 %

-
Processing

Software
NameClassification
MERLOTphasing
CNSrefinement
CAD4data reduction
MOLENdata scaling
RefinementResolution: 1.75→20 Å / Rfactor Rfree error: 0.017 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.227 540 9.9 %RANDOM
Rwork0.18 ---
obs-5480 75.1 %-
Displacement parametersBiso mean: 7.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20 Å2-0.39 Å2
2---0.85 Å20 Å2
3---0.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a-0.13 Å
Refinement stepCycle: LAST / Resolution: 1.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms569 0 0 153 722
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_improper_angle_d1.24
LS refinement shellResolution: 1.75→1.86 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.296 67 10.7 %
Rwork0.286 559 -
obs--53.2 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2HYP.PAR3
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor obs: 0.18 / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.24
LS refinement shell
*PLUS
Rfactor Rfree: 0.296 / Rfactor Rwork: 0.286

+
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