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

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Basic information

Entry
Database: PDB / ID: 3ent
TitleCrystal structure of Nitrollin, a betagamma-crystallin from Nitrosospira multiformis-in alternate space group (P65)
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.14 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 1.3Oct 16, 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
B: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)26,6502
Polymers26,6502
Non-polymers00
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-25 kcal/mol
Surface area11190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.451, 60.451, 150.759
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Putative uncharacterized protein / Nitrollin


Mass: 13325.176 Da / Num. of mol.: 2
Fragment: single domain betagamma-crystallin, residues 24-140
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.: 177 / 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: 2.98 Å3/Da / Density % sol: 58.78 % / Mosaicity: 0.443 °
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 26% PEG3350, 0.2M NaCl, 0.1M Tris, pH 8.0, VAPOR DIFFUSION, HANGING 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 28, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.14→25 Å / Num. obs: 16884 / % possible obs: 98.1 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.056 / Χ2: 0.765 / Net I/σ(I): 26.659
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.14-2.223.80.3914140.61982.9
2.22-2.315.50.40816940.62698.9
2.31-2.417.20.35817350.601100
2.41-2.5480.27417100.636100
2.54-2.78.10.20617010.648100
2.7-2.98.20.1317370.654100
2.9-3.28.20.07817120.681100
3.2-3.668.30.04817140.777100
3.66-4.68.30.03117341.083100
4.6-258.30.02617331.13198.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.5 Å24.73 Å
Translation3.5 Å24.73 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.14→25 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.828 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.239 848 4.9 %
Rwork0.207 --
obs-16849 98.2 %
Solvent computationBsol: 49.319 Å2
Displacement parametersBiso max: 73.58 Å2 / Biso mean: 39.682 Å2 / Biso min: 21.9 Å2
Baniso -1Baniso -2Baniso -3
1--5.35 Å2-5.616 Å20 Å2
2---5.35 Å20 Å2
3---10.701 Å2
Refinement stepCycle: LAST / Resolution: 2.14→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1878 0 0 177 2055
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0065461.5
X-RAY DIFFRACTIONc_angle_deg1.265382
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param

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