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- PDB-3cs5: NblA protein from Synechococcus elongatus PCC 7942 -

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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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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Experimental details

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Experiment

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

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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

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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

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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

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