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- PDB-2hnw: Crystal Structure of the F91STOP mutant of des1-6 Bovine Neurophy... -

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Basic information

Entry
Database: PDB / ID: 2hnw
TitleCrystal Structure of the F91STOP mutant of des1-6 Bovine Neurophysin-I, unliganded state
ComponentsOxytocin-neurophysin 1
KeywordsPEPTIDE BINDING PROTEIN / unliganded bovine neurophysin-I / des1-6 / F91STOP mutations / inter-domain loop / disulfides / beta sheet / 3 / 10 helix / subunit interface
Function / homology
Function and homology information


Vasopressin-like receptors / oxytocin receptor binding / neurohypophyseal hormone activity / V1A vasopressin receptor binding / neuropeptide hormone activity / G alpha (q) signalling events / secretory granule / response to estrogen / positive regulation of cold-induced thermogenesis / extracellular space
Similarity search - Function
Neurophysin II; Chain A / Neurohypophysial hormone domain / Neurohypophysial hormone / Neurohypophysial hormone, conserved site / Neurohypophysial hormone domain superfamily / Neurohypophysial hormones, C-terminal Domain / Neurohypophysial hormones, N-terminal Domain / Neurohypophysial hormones signature. / Neurohypophysial hormones / Sandwich / Mainly Beta
Similarity search - Domain/homology
Oxytocin-neurophysin 1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsLi, X. / Lee, H. / Wu, J. / Breslow, E.
CitationJournal: Protein Sci. / Year: 2007
Title: Contributions of the interdomain loop, amino terminus, and subunit interface to the ligand-facilitated dimerization of neurophysin: crystal structures and mutation studies of bovine neurophysin-I.
Authors: Li, X. / Lee, H. / Wu, J. / Breslow, E.
History
DepositionJul 13, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 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

Downloads & links

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Assembly

Deposited unit
A: Oxytocin-neurophysin 1
B: Oxytocin-neurophysin 1
C: Oxytocin-neurophysin 1
D: Oxytocin-neurophysin 1
E: Oxytocin-neurophysin 1


Theoretical massNumber of molelcules
Total (without water)40,3315
Polymers40,3315
Non-polymers00
Water00
1
A: Oxytocin-neurophysin 1
B: Oxytocin-neurophysin 1


Theoretical massNumber of molelcules
Total (without water)16,1322
Polymers16,1322
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Oxytocin-neurophysin 1
D: Oxytocin-neurophysin 1


Theoretical massNumber of molelcules
Total (without water)16,1322
Polymers16,1322
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Oxytocin-neurophysin 1

E: Oxytocin-neurophysin 1


Theoretical massNumber of molelcules
Total (without water)16,1322
Polymers16,1322
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_766-x+2,-x+y+1,-z+11
Unit cell
Length a, b, c (Å)117.891, 117.891, 66.845
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
DetailsThe biological unit is a dimer. There are 2.5 biological units per asymmetric unit. The complete dimers are comprised of chains A & B and chains C & D. Chain E is half of a dimer from another asymmetric unit.

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Components

#1: Protein
Oxytocin-neurophysin 1


Mass: 8066.139 Da / Num. of mol.: 5 / Fragment: Residues 38-117
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: OXT / Plasmid: pTHMa30-51 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)p Lys S / References: UniProt: P01175

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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: 3.32 Å3/Da / Density % sol: 62.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.5 M sodium chloride, 11%v/v ethanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 5, 2005
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.9→23.84 Å / Num. obs: 22559 / % possible obs: 97.8 % / Rmerge(I) obs: 0.073 / Χ2: 1.044 / Net I/σ(I): 10.3
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2% possible all
2.9-30.38222371.02498.1
3-3.120.27722751.03598.1
3.12-3.270.18622661.04998.4
3.27-3.440.14522801.07198.4
3.44-3.650.11521991.01496.2
3.65-3.930.10222490.9796.7
3.93-4.330.05922531.08198.6
4.33-4.950.05122961.07798.7
4.95-6.230.05922671.10198.3
6.23-300.05422371.00597

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HNU

2hnu


Resolution: 2.9→23.84 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 316465.062 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.321 1052 4.8 %RANDOM
Rwork0.245 ---
obs-21906 95.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.951 Å2 / ksol: 0.275 e/Å3
Displacement parametersBiso mean: 81.5 Å2
Baniso -1Baniso -2Baniso -3
1--8.8 Å20.42 Å20 Å2
2---8.8 Å20 Å2
3---17.61 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.61 Å0.43 Å
Luzzati d res low-30 Å
Luzzati sigma a0.54 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 2.9→23.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2755 0 0 0 2755
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d26.3
X-RAY DIFFRACTIONc_improper_angle_d1.31
X-RAY DIFFRACTIONc_mcbond_it12.521.5
X-RAY DIFFRACTIONc_mcangle_it19.432
X-RAY DIFFRACTIONc_scbond_it16.812
X-RAY DIFFRACTIONc_scangle_it23.042.5
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.38 164 4.7 %
Rwork0.353 3337 -
obs-3501 91.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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