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- PDB-2hnu: Crystal Structure of a Dipeptide Complex of Bovine Neurophysin-I -

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Basic information

Entry
Database: PDB / ID: 2hnu
TitleCrystal Structure of a Dipeptide Complex of Bovine Neurophysin-I
ComponentsOxytocin-neurophysin 1
KeywordsPEPTIDE BINDING PROTEIN / Neurophysin / ligand-facilitated dimerization / inter-domain loop / amino-terminus / subunit interface / hydrogen bonding
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
PHENYLALANINE / TYROSINE / Oxytocin-neurophysin 1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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 ...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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: Oxytocin-neurophysin 1
B: Oxytocin-neurophysin 1
C: Oxytocin-neurophysin 1
D: Oxytocin-neurophysin 1
E: Oxytocin-neurophysin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,54815
Polymers40,8165
Non-polymers1,73210
Water1,29772
1
A: Oxytocin-neurophysin 1
B: Oxytocin-neurophysin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0196
Polymers16,3272
Non-polymers6934
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Oxytocin-neurophysin 1
D: Oxytocin-neurophysin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0196
Polymers16,3272
Non-polymers6934
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Oxytocin-neurophysin 1
hetero molecules

E: Oxytocin-neurophysin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0196
Polymers16,3272
Non-polymers6934
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_556x,x-y,-z+4/31
Unit cell
Length a, b, c (Å)111.157, 111.157, 127.241
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
DetailsThe biological unit is a dimer. There are 2.5 biological units per asymmetric unit (chains A & B and chains C & D and chain E

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Components

#1: Protein
Oxytocin-neurophysin 1


Mass: 8163.254 Da / Num. of mol.: 5 / Fragment: Residues 38-118
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
#2: Chemical
ChemComp-PHE / PHENYLALANINE


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C9H11NO2
#3: Chemical
ChemComp-TYR / TYROSINE


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C9H11NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.67 Å3/Da / Density % sol: 53.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2 M ammonium acetate, 0.1 M trisodium citrate dihydrate, 60% PEG4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.541 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 7, 2004 / Details: VariMax-HR
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 59209 / % possible obs: 99.3 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.067 / Χ2: 1.1 / Net I/σ(I): 13.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2-2.075.60.58759101.15299
2.07-2.156.30.47559231.14899.9
2.15-2.256.50.34559691.16799.9
2.25-2.376.60.2659481.15399.9
2.37-2.526.70.20259641.08699.9
2.52-2.716.90.13359451.199.8
2.71-2.997.30.08759211.08799.6
2.99-3.4280.05859231.09299.4
3.42-4.318.40.03858871.04298.7
4.31-508.60.02858191.03397

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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 1JK6

1jk6


Resolution: 2→28.65 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 298758.312 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.245 2805 4.9 %RANDOM
Rwork0.219 ---
obs-56962 95.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.183 Å2 / ksol: 0.383 e/Å3
Displacement parametersBiso mean: 34.9 Å2
Baniso -1Baniso -2Baniso -3
1-3.35 Å23.9 Å20 Å2
2--3.35 Å20 Å2
3----6.71 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.25 Å
Luzzati d res low-30 Å
Luzzati sigma a0.2 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2→28.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2910 0 0 72 2982
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_improper_angle_d1.02
X-RAY DIFFRACTIONc_mcbond_it2.811.5
X-RAY DIFFRACTIONc_mcangle_it4.532
X-RAY DIFFRACTIONc_scbond_it5.72
X-RAY DIFFRACTIONc_scangle_it8.62.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.28 455 5.1 %
Rwork0.258 8529 -
obs-8984 90.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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