[English] 日本語
Yorodumi
- PDB-5x3m: crystal structure of p-Ub-S65-NH2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5x3m
Titlecrystal structure of p-Ub-S65-NH2
Components
  • D-ubiquitin
  • Polyubiquitin-B
KeywordsPROTEIN BINDING / Ubiquitin / Synthesis / phosphorylation
Function / homology
Function and homology information


symbiont entry into host cell via disruption of host cell glycocalyx / symbiont entry into host cell via disruption of host cell envelope / virus tail
Similarity search - Function
Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Pectin lyase fold / Pectin lyase fold/virulence factor / Ubiquitin family
Similarity search - Domain/homology
polypeptide(D) / polypeptide(D) (> 10) / Tail fiber
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.818 Å
AuthorsMan, P. / Shuai, G. / Qian, Q. / Lei, L.
CitationJournal: To Be Published
Title: Structure of p-Ub-S65-NH2 at 1.82 Angstroms resolution
Authors: Man, P. / Shuai, G. / Qian, Q. / Lei, L.
History
DepositionFeb 6, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 9, 2022Group: Database references / Category: database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Polyubiquitin-B
D: D-ubiquitin


Theoretical massNumber of molelcules
Total (without water)17,2512
Polymers17,2512
Non-polymers00
Water2,846158
1
A: Polyubiquitin-B

D: D-ubiquitin


Theoretical massNumber of molelcules
Total (without water)17,2512
Polymers17,2512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area1410 Å2
ΔGint-11 kcal/mol
Surface area7920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.914, 29.969, 39.726
Angle α, β, γ (deg.)81.91, 72.38, 62.43
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Polyubiquitin-B


Mass: 8656.811 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P0CG47
#2: Protein D-ubiquitin


Mass: 8593.780 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: D-Ub-S65E-NH2 / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 1.69 Å3/Da / Density % sol: 27.04 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2M Lithium Sulfate monohydrate, 0.1M HEPES pH 7.5, 25%(w/v) Polyethylene Glycol 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jan 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.818→26.565 Å / Num. obs: 9443 / % possible obs: 82.8 % / Redundancy: 3.5 % / Net I/σ(I): 6.8

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.818→26.565 Å / SU ML: 0.16 / Cross valid method: NONE / σ(F): 1.98 / Phase error: 31.82 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2705 498 5.28 %
Rwork0.2062 --
obs0.2096 9435 93.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.818→26.565 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1191 0 0 158 1349
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071233
X-RAY DIFFRACTIONf_angle_d1.0671670
X-RAY DIFFRACTIONf_dihedral_angle_d11.68794
X-RAY DIFFRACTIONf_chiral_restr0.072198
X-RAY DIFFRACTIONf_plane_restr0.005217
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8184-2.00140.24751320.18262093X-RAY DIFFRACTION87
2.0014-2.29080.2492970.19822244X-RAY DIFFRACTION92
2.2908-2.88570.27031260.22542273X-RAY DIFFRACTION95
2.8857-26.5680.28461430.20552327X-RAY DIFFRACTION97

+
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