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- PDB-2q8v: NblA protein from T. vulcanus crystallized with urea -

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Basic information

Entry
Database: PDB / ID: 2q8v
TitleNblA protein from T. vulcanus crystallized with urea
ComponentsNblA protein
KeywordsPROTEIN BINDING / Phycobilisome / nutrient starvation / disassembly / 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 / UREA / NblA
Function and homology information
Biological speciesThermosynechococcus vulcanus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD/Molecular Replacement / Resolution: 2.5 Å
AuthorsAdir, N. / Dines, M.
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
DepositionJun 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NblA protein
B: NblA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0554
Polymers14,9352
Non-polymers1202
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint-34 kcal/mol
Surface area7520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.265, 43.265, 149.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein NblA protein


Mass: 7467.691 Da / Num. of mol.: 2
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: Chemical ChemComp-URE / UREA


Mass: 60.055 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH4N2O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.7 Å3/Da / Density % sol: 54.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 25% elthelene glycol, 2M Urea, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF BM30A10.97913
SYNCHROTRONESRF ID14-120.9792
DetectorType: ADSC QUANTUM 4 / Detector: CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979131
20.97921
ReflectionResolution: 2.5→50 Å / Num. obs: 6108 / % possible obs: 99.8 % / Observed criterion σ(I): 2.5 / Redundancy: 6.2 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 19.1
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.326 / Mean I/σ(I) obs: 4.4 / Num. unique all: 849 / Rsym value: 0.358 / % possible all: 100

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Processing

Software
NameVersionClassification
DNAdata collection
CCP4model building
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
CCP4phasing
RefinementMethod to determine structure: SAD/Molecular Replacement
Starting model: 1OJH

1ojh


Resolution: 2.5→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.264 984 -random
Rwork0.245 ---
obs-6108 100 %-
Displacement parametersBiso mean: 36.4 Å2
Baniso -1Baniso -2Baniso -3
1--6.085 Å2-7.701 Å20 Å2
2---6.085 Å20 Å2
3---12.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms843 0 8 16 867
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.09
X-RAY DIFFRACTIONc_bond_d0.0096
X-RAY DIFFRACTIONc_dihedral_angle_d20.2
X-RAY DIFFRACTIONc_improper_angle_d1.72

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