[English] 日本語
Yorodumi
- PDB-6uvi: Crystal structure of alr1298, a pentapeptide repeat protein from ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6uvi
TitleCrystal structure of alr1298, a pentapeptide repeat protein from Nostoc Pcc 7120, determined at 2.3 Angstrom resolution
ComponentsAlr1298 protein
KeywordsUNKNOWN FUNCTION / pentapeptide repeat / protein repeat / five residue right-handed-beta helix
Function / homologyPentapeptide repeats (8 copies) / Pentapeptide repeat / Alr1298 protein
Function and homology information
Biological speciesNostoc sp. PCC 7120 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKennedy, M.A. / Zhang, R.
CitationJournal: Proteins / Year: 2020
Title: Crystal structure of Alr1298, a pentapeptide repeat protein from the cyanobacterium Nostoc sp. PCC 7120, determined at 2.1 angstrom resolution.
Authors: Zhang, R. / Ni, S. / Kennedy, M.A.
History
DepositionNov 2, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 12, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alr1298 protein
B: Alr1298 protein


Theoretical massNumber of molelcules
Total (without water)41,9092
Polymers41,9092
Non-polymers00
Water1,22568
1
A: Alr1298 protein


Theoretical massNumber of molelcules
Total (without water)20,9551
Polymers20,9551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Alr1298 protein


Theoretical massNumber of molelcules
Total (without water)20,9551
Polymers20,9551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.762, 85.922, 95.686
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Alr1298 protein


Mass: 20954.623 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. PCC 7120 (bacteria) / Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / Gene: alr1298 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8YXB7
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.24 Å3/Da / Density % sol: 45.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium acetate, 0.1 M Sodium acetate trihydrate pH 4.6, 30% w/v Polyethylene glycol 4,000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.1→31.32 Å / Num. obs: 22287 / % possible obs: 98.03 % / Redundancy: 2 % / Biso Wilson estimate: 40.41 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.01859 / Rpim(I) all: 0.01859 / Rrim(I) all: 0.02629 / Net I/σ(I): 18.53
Reflection shellResolution: 2.1→2.21 Å / Rmerge(I) obs: 0.065 / Mean I/σ(I) obs: 17.7 / Num. unique obs: 22336 / Rpim(I) all: 0.028 / Rrim(I) all: 0.071

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDS1.1.7data reduction
Aimless0.7.1data scaling
PHENIX1.13_2998phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6UV7
Resolution: 2.1→31.32 Å / SU ML: 0.3238 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.8294
RfactorNum. reflection% reflection
Rfree0.2744 1996 8.97 %
Rwork0.2085 --
obs0.2144 22261 98.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 60.16 Å2
Refinement stepCycle: LAST / Resolution: 2.1→31.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2413 0 0 68 2481
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01182442
X-RAY DIFFRACTIONf_angle_d1.19573286
X-RAY DIFFRACTIONf_chiral_restr0.0547372
X-RAY DIFFRACTIONf_plane_restr0.0064438
X-RAY DIFFRACTIONf_dihedral_angle_d15.38331490
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.35051380.31511404X-RAY DIFFRACTION98.09
2.15-2.210.34731410.31331427X-RAY DIFFRACTION98.25
2.21-2.280.40741390.30931408X-RAY DIFFRACTION96.81
2.28-2.350.36291380.28391404X-RAY DIFFRACTION97.29
2.35-2.430.3631420.26541443X-RAY DIFFRACTION98.33
2.43-2.530.32921420.26881441X-RAY DIFFRACTION98.51
2.53-2.650.3011410.25011426X-RAY DIFFRACTION99.18
2.65-2.790.33281430.25451460X-RAY DIFFRACTION98.89
2.79-2.960.34611370.25091392X-RAY DIFFRACTION95.32
2.96-3.190.30041440.24951463X-RAY DIFFRACTION99.08
3.19-3.510.27981450.22551479X-RAY DIFFRACTION99.33
3.51-4.010.25191460.17891484X-RAY DIFFRACTION99.45
4.01-5.050.17841470.14831487X-RAY DIFFRACTION97.49
5.05-31.320.26671530.16741547X-RAY DIFFRACTION97.31

+
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