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- PDB-2qdo: NblA protein from T. vulcanus -

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Basic information

Entry
Database: PDB / ID: 2qdo
TitleNblA protein from T. vulcanus
ComponentsNblA protein
KeywordsPHOTOSYNTHESIS / Phycobilisome / nutrient starvation / bleaching
Function / homologyPhycobilisome degradation protein NblA / Phycobilisome degradation protein NblA / Phycobilisome degradation protein NblA superfamily / Phycobilisome degradation protein nblA / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / NblA
Function and homology information
Biological speciesThermosynechococcus vulcanus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsDines, M. / Adir, N.
CitationJournal: 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.
History
DepositionJun 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 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: NblA protein
B: NblA protein
C: NblA protein
D: NblA protein


Theoretical massNumber of molelcules
Total (without water)25,3904
Polymers25,3904
Non-polymers00
Water32418
1
C: NblA protein
D: NblA protein


Theoretical massNumber of molelcules
Total (without water)12,6952
Polymers12,6952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-30 kcal/mol
Surface area7490 Å2
MethodPISA
2
A: NblA protein
B: NblA protein


Theoretical massNumber of molelcules
Total (without water)12,6952
Polymers12,6952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-30 kcal/mol
Surface area7350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.190, 42.390, 50.560
Angle α, β, γ (deg.)69.00, 83.36, 61.25
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
NblA protein / Phycobilisome degradation protein


Mass: 6347.477 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus vulcanus (bacteria)
Gene: nbla / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / References: UniProt: A7LBW5*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.91 Å3/Da / Density % sol: 57.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 25% ethylene glycol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.5→47 Å / Num. all: 9900 / Num. obs: 9900 / % possible obs: 96.7 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 19.5

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Q8V

2q8v


Resolution: 2.5→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.279 871 -random
Rwork0.248 ---
all-9878 --
obs-8366 84.7 %-
Displacement parametersBiso mean: 41.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.65 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1697 0 0 18 1715
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.61
X-RAY DIFFRACTIONc_bond_d0.0086
X-RAY DIFFRACTIONc_dihedral_angle_d20.9
X-RAY DIFFRACTIONc_improper_angle_d0.91

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