[English] 日本語
Yorodumi
- PDB-3a19: Structure of (PPG)4-OOG-(PPG)4_H monoclinic, twinned crystal -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3a19
TitleStructure of (PPG)4-OOG-(PPG)4_H monoclinic, twinned crystal
Componentscollagen-like peptide
KeywordsSTRUCTURAL PROTEIN / collagen / triple-helix / twinned crystal
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsOkuyama, K. / Morimoto, T. / Hyakutake, M. / Wu, G. / Mizuno, K. / Bachinger, H.P.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2010
Title: Two crystal modifications of (Pro-Pro-Gly)4-Hyp-Hyp-Gly-(Pro-Pro-Gly)4 reveal the puckering preference of Hyp(X) in the Hyp(X):Hyp(Y) and Hyp(X):Pro(Y) stacking pairs in collagen helices.
Authors: Okuyama, K. / Morimoto, T. / Narita, H. / Kawaguchi, T. / Mizuno, K. / Bachinger, H.P. / Wu, G. / Noguchi, K.
History
DepositionMar 28, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 17, 2014Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: collagen-like peptide
B: collagen-like peptide
C: collagen-like peptide
D: collagen-like peptide
E: collagen-like peptide
F: collagen-like peptide


Theoretical massNumber of molelcules
Total (without water)13,8696
Polymers13,8696
Non-polymers00
Water4,270237
1
A: collagen-like peptide
B: collagen-like peptide
C: collagen-like peptide


Theoretical massNumber of molelcules
Total (without water)6,9353
Polymers6,9353
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-26 kcal/mol
Surface area4120 Å2
MethodPISA
2
D: collagen-like peptide
E: collagen-like peptide
F: collagen-like peptide


Theoretical massNumber of molelcules
Total (without water)6,9353
Polymers6,9353
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-27 kcal/mol
Surface area4070 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9550 Å2
ΔGint-68 kcal/mol
Surface area7180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)23.649, 26.928, 79.656
Angle α, β, γ (deg.)90.00, 89.93, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein/peptide
collagen-like peptide


Mass: 2311.547 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: THIS PEPTIDE WAS CHEMICALLY SYSTHESIZED.
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS SEQUENCE ADOPTS A TRIPLE-HELICAL STRUCTURE SIMILAR TO THE COLLAGEN-HELIX.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.8 Å3/Da / Density % sol: 32.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 16.25%(w/v) PEG 1000, 0.05M acetate buffer, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

-
Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 25, 2004 / Details: 1.1 M bent-plane mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 14850 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.081
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.35 / % possible all: 99.9

-
Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CUO

2cuo


Resolution: 1.55→20 Å / Num. parameters: 4666 / Num. restraintsaints: 4206 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: THE STRUCTURE WAS REFINED UNDER THE TWINNING OPERATOR (H,-K,-L) AND THE TWINNING FRACTION 0.421 USING THE TWINNED DATA.
RfactorNum. reflection% reflectionSelection details
Rfree0.2044 736 -RANDOM
Rwork0.1663 ---
obs-14833 94.2 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1165
Refinement stepCycle: LAST / Resolution: 1.55→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms928 0 0 237 1165
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.008
X-RAY DIFFRACTIONs_angle_d0.023
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0269
X-RAY DIFFRACTIONs_zero_chiral_vol0.052
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.052
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.005
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.067
X-RAY DIFFRACTIONs_approx_iso_adps0
LS refinement shell
Resolution (Å)Rfactor RworkRefine-IDNum. reflection obsTotal num. of bins used
1.54-1.610.219X-RAY DIFFRACTION14806
1.61-1.670.208X-RAY DIFFRACTION14096
1.67-1.750.186X-RAY DIFFRACTION13946
1.75-1.840.182X-RAY DIFFRACTION13836
1.84-1.950.159X-RAY DIFFRACTION13966
1.95-2.110.154X-RAY DIFFRACTION14266

+
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