[English] 日本語
Yorodumi
- PDB-3cs5: NblA protein from Synechococcus elongatus PCC 7942 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3cs5
TitleNblA protein from Synechococcus elongatus PCC 7942
ComponentsPhycobilisome degradation protein nblA
KeywordsPHOTOSYNTHESIS / phycobilisome / nutrient stress / bleaching / helix-turn-helix / partial merohedral twinning
Function / homologyPhycobilisome degradation protein NblA / Phycobilisome degradation protein NblA / Phycobilisome degradation protein NblA superfamily / Phycobilisome degradation protein nblA / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / Phycobilisome degradation protein NblA
Function and homology information
Biological speciesSynechococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsDines, M. / Sendersky, E. / Schwarz, R. / Adir, N.
Citation
Journal: J.Biol.Chem. / Year: 2008
Title: Structural, Functional, and Mutational Analysis of the NblA Protein Provides Insight into Possible Modes of Interaction with the Phycobilisome
Authors: Dines, M. / Sendersky, E. / David, L. / Schwarz, R. / Adir, N.
#1: Journal: J.Struct.Biol. / Year: 2007
Title: Crystallization of sparingly soluble stress-related proteins from cyanobacteria by controlled urea solublization
Authors: Dines, M. / Sendersky, E. / Schwarz, R. / Adir, N.
History
DepositionApr 9, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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: Phycobilisome degradation protein nblA
B: Phycobilisome degradation protein nblA
C: Phycobilisome degradation protein nblA
D: Phycobilisome degradation protein nblA


Theoretical massNumber of molelcules
Total (without water)28,2404
Polymers28,2404
Non-polymers00
Water48627
1
A: Phycobilisome degradation protein nblA
B: Phycobilisome degradation protein nblA


Theoretical massNumber of molelcules
Total (without water)14,1202
Polymers14,1202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-23.1 kcal/mol
Surface area7390 Å2
MethodPISA
2
C: Phycobilisome degradation protein nblA
D: Phycobilisome degradation protein nblA


Theoretical massNumber of molelcules
Total (without water)14,1202
Polymers14,1202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-23 kcal/mol
Surface area7230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.080, 78.080, 70.678
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4
Components on special symmetry positions
IDModelComponents
11B-60-

HOH

-
Components

#1: Protein
Phycobilisome degradation protein nblA


Mass: 7060.076 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus sp. (bacteria) / Strain: PCC 7942 / Gene: nblA / Plasmid: pQE-70 / Production host: Escherichia coli (E. coli) / References: UniProt: P35087
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 3.81 Å3/Da / Density % sol: 67.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 25% ethylene glycol, pH8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
merohedral11h,k,l10.521
merohedral11h,-k,-l20.479
ReflectionResolution: 2.2→20 Å / Num. obs: 21001 / % possible obs: 96.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 20.1 Å2 / Rsym value: 0.057 / Net I/σ(I): 9.75

-
Processing

Software
NameClassification
DNAdata collection
PHASERphasing
SHELXL-97refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Q8V

2q8v


Resolution: 2.2→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 4 / Stereochemistry target values: Engh & Huber
Details: This is a twinned structure, the detwin fraction is 0.479 and operator is 'h, -k, -l'.
RfactorNum. reflectionSelection details
Rfree0.3466 1844 Random
Rwork0.2476 --
all-21001 -
obs-18211 -
Displacement parametersBiso mean: 27.5 Å2
Refine analyzeLuzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.509 Å
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1644 0 0 27 1671
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.022
X-RAY DIFFRACTIONs_angle_d1.9

+
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://pdbjlvh1.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