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- PDB-2hnv: Crystal Structure of a Dipeptide Complex of the Q58V Mutant of Bo... -

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Basic information

Entry
Database: PDB / ID: 2hnv
TitleCrystal Structure of a Dipeptide Complex of the Q58V Mutant of Bovine Neurophysin-I
ComponentsOxytocin-neurophysin 1
KeywordsPEPTIDE BINDING PROTEIN / protein-pepide complex / Q58V mutant / inter-domain loop / beta sheet / 3 / 10 helix
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 / Resolution: 2.5 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 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,40315
Polymers40,6715
Non-polymers1,73210
Water52229
1
A: Oxytocin-neurophysin 1
B: Oxytocin-neurophysin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9616
Polymers16,2692
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)16,9616
Polymers16,2692
Non-polymers6934
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-14 kcal/mol
Surface area8220 Å2
MethodPISA
3
E: Oxytocin-neurophysin 1
hetero molecules

E: Oxytocin-neurophysin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9616
Polymers16,2692
Non-polymers6934
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_545x,x-y-1,-z+1/31
Unit cell
Length a, b, c (Å)110.904, 110.904, 126.682
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. 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: 8134.256 Da / Num. of mol.: 5 / Fragment: Residues 38-118 / Mutation: Q58V
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 / Phenylalanine


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


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


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.65 Å3/Da / Density % sol: 53.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.2 M calcium chloride dihydrate, 0.1 M sodium acetate trihydrate, 22% v/v isopropanol, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.541 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 1, 2005 / Details: VariMax-HR
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 2.5→38.66 Å / Num. obs: 17407 / % possible obs: 99.6 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.074 / Χ2: 1.002 / Net I/σ(I): 15.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.5-2.596.80.67817100.907100
2.59-2.6970.44517050.946100
2.69-2.827.40.34416910.989100
2.82-2.967.80.22717141.052100
2.96-3.158.20.14217270.978100
3.15-3.398.70.10317180.987100
3.39-3.738.60.10117250.99399.7
3.73-4.278.70.07417631.02199.7
4.27-5.389.20.04217791.07999.6
5.38-508.70.04118751.02197.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
PDB_EXTRACT2data extraction
RefinementStarting model: PDB ENTRY 2HNU

2hnu


Resolution: 2.5→22.04 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 623573.625 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.282 736 4.9 %RANDOM
Rwork0.218 ---
obs-15132 91.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.583 Å2 / ksol: 0.335 e/Å3
Displacement parametersBiso mean: 56.9 Å2
Baniso -1Baniso -2Baniso -3
1-8.44 Å28.41 Å20 Å2
2--8.44 Å20 Å2
3----16.89 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.33 Å
Luzzati d res low-30 Å
Luzzati sigma a0.45 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.5→22.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2900 0 0 29 2929
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d24.9
X-RAY DIFFRACTIONc_improper_angle_d1.08
X-RAY DIFFRACTIONc_mcbond_it5.351.5
X-RAY DIFFRACTIONc_mcangle_it8.622
X-RAY DIFFRACTIONc_scbond_it8.462
X-RAY DIFFRACTIONc_scangle_it12.272.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.392 117 5.1 %
Rwork0.299 2161 -
obs-2278 85.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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