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- PDB-3enu: Crystal structure of Nitrollin, a betagamma-crystallin from Nitro... -

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Basic information

Entry
Database: PDB / ID: 3enu
TitleCrystal structure of Nitrollin, a betagamma-crystallin from Nitrosospira multiformis
ComponentsPutative uncharacterized protein
KeywordsSTRUCTURAL PROTEIN / betagamma crystallin
Function / homology
Function and homology information


cell-cell adhesion / membrane
Similarity search - Function
Calcium-dependent cell adhesion molecule, N-terminal / Beta/Gamma crystallin / Crystallins / Gamma-B Crystallin; domain 1 / Gamma-crystallin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Beta/Gamma crystallin
Similarity search - Component
Biological speciesNitrosospira multiformis (bacteria)
MethodX-RAY DIFFRACTION / MIRAS / Resolution: 1.86 Å
AuthorsAravind, P. / Sankaranarayanan, R.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Three-dimensional domain swapping in nitrollin, a single-domain betagamma-crystallin from Nitrosospira multiformis, controls protein conformation and stability but not dimerization
Authors: Aravind, P. / Suman, S.K. / Mishra, A. / Sharma, Y. / Sankaranarayanan, R.
History
DepositionSep 26, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 31, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)12,9501
Polymers12,9501
Non-polymers00
Water2,252125
1
A: Putative uncharacterized protein

A: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)25,8992
Polymers25,8992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area3070 Å2
ΔGint-28 kcal/mol
Surface area10430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.257, 80.903, 32.137
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Putative uncharacterized protein / Nitrollin


Mass: 12949.712 Da / Num. of mol.: 1
Fragment: single domain betagamma-crystallin, residues 27-140
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitrosospira multiformis (bacteria) / Strain: ATCC 25196 / Gene: 3786576 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2YAE2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.32 Å3/Da / Density % sol: 47.02 % / Mosaicity: 0.486 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 20% PEG3350, 0.2M Naformate, vapor diffusion, sitting drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: MAR 345dtb / Detector: IMAGE PLATE / Date: Oct 4, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.86→25 Å / Num. obs: 10654 / % possible obs: 99.8 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.046 / Χ2: 1.109 / Net I/σ(I): 40.15
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.86-1.936.20.1210150.86897.8
1.93-26.60.0910450.916100
2-2.096.60.07710440.954100
2.09-2.216.70.06810400.958100
2.21-2.346.70.05910631.06100
2.34-2.526.70.05410451.031100
2.52-2.786.80.0510541.178100
2.78-3.186.70.04210871.15100
3.18-46.60.03310921.28699.8
4-256.30.0311691.625100

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Phasing

PhasingMethod: MIRAS
Phasing MIRResolution: 2.4→20 Å / FOM: 0.51 / Reflection: 5062
Phasing MIR der
IDDer set-ID
11
21
31
Phasing MIR der site
IDDer-IDBiso (Å)Atom type symbolFract xFract yFract zOccupancy
1115.4758Au0.62360.33610.26330.3279
1236.583Au0.17830.13760.41520.5211
215.1919I0.72020.180.37470.2014
2260I0.64290.34480.27740.5365
231I0.70470.30930.18050.1055
Phasing MIR shell
Resolution (Å)FOMReflection
8.22-200.74286
5.33-8.220.66432
4.21-5.330.56552
3.59-4.210.52626
3.18-3.590.48702
2.88-3.180.49769
2.66-2.880.45804
2.48-2.660.44891

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.1phasing
CNSrefinement
PDB_EXTRACT3.006data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: MIRAS / Resolution: 1.86→25 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.874 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.219 539 5.1 %
Rwork0.181 --
obs-10624 99.7 %
Solvent computationBsol: 42.54 Å2
Displacement parametersBiso max: 44.65 Å2 / Biso mean: 11.501 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1--0.403 Å20 Å20 Å2
2--0.1 Å20 Å2
3---0.304 Å2
Refinement stepCycle: LAST / Resolution: 1.86→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms914 0 0 125 1039
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.0721.5
X-RAY DIFFRACTIONc_scbond_it2.1792
X-RAY DIFFRACTIONc_mcangle_it1.5432
X-RAY DIFFRACTIONc_scangle_it3.2512.5
X-RAY DIFFRACTIONc_bond_d0.004884
X-RAY DIFFRACTIONc_angle_deg1.34785
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param

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