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- PDB-1npo: BOVINE NEUROPHYSIN II COMPLEX WITH OXYTOCIN -

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Basic information

Entry
Database: PDB / ID: 1npo
TitleBOVINE NEUROPHYSIN II COMPLEX WITH OXYTOCIN
Components
  • (NEUROPHYSIN II) x 2
  • OXYTOCIN
KeywordsCOMPLEX (HORMONE TRANSPORT/HORMONE) / COMPLEX (HORMONE TRANSPORT-HORMONE) / HYPOTHALAMUS / COMPLEX (HORMONE TRANSPORT-HORMONE) complex
Function / homology
Function and homology information


neurohypophyseal hormone activity / V1A vasopressin receptor binding / neuropeptide hormone activity / vasoconstriction / secretory granule / 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
Vasopressin-neurophysin 2-copeptin
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsRose, J.P. / Wang, B.-C.
Citation
Journal: Nat.Struct.Biol. / Year: 1996
Title: Crystal structure of the neurophysin-oxytocin complex.
Authors: Rose, J.P. / Wu, C.K. / Hsiao, C.D. / Breslow, E. / Wang, B.C.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1991
Title: Crystal Structure of a Bovine Neurophysin II Dipeptide Complex at 2.8 A Determined from the Single-Wavelength Anomalous Scattering Signal of an Incorporated Iodine Atom
Authors: Chen, L.Q. / Rose, J.P. / Breslow, E. / Yang, D. / Chang, W.R. / Furey Junior, W.F. / Sax, M. / Wang, B.C.
#2: Journal: Eur.J.Biochem. / Year: 1988
Title: Crystals of Modified Bovine Neurophysin II
Authors: Rose, J.P. / Yang, D. / Yoo, C.S. / Sax, M. / Breslow, E. / Wang, B.C.
#3: Journal: J.Mol.Biol. / Year: 1979
Title: Crystals of a Bovine Neurophysin II-Dipeptide Amide Complex
Authors: Yoo, C.S. / Wang, B.C. / Sax, M. / Breslow, E.
History
DepositionFeb 1, 1996Processing site: BNL
Revision 1.0Feb 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NEUROPHYSIN II
B: OXYTOCIN
C: NEUROPHYSIN II
D: OXYTOCIN


Theoretical massNumber of molelcules
Total (without water)21,7434
Polymers21,7434
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-15 kcal/mol
Surface area8620 Å2
MethodPISA
2
A: NEUROPHYSIN II
B: OXYTOCIN

A: NEUROPHYSIN II
B: OXYTOCIN

C: NEUROPHYSIN II
D: OXYTOCIN

C: NEUROPHYSIN II
D: OXYTOCIN


Theoretical massNumber of molelcules
Total (without water)43,4868
Polymers43,4868
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
crystal symmetry operation3_545-y+1/2,x-1/2,z+1/41
crystal symmetry operation5_655-x+3/2,y+1/2,-z+1/41
Buried area6320 Å2
ΔGint-45 kcal/mol
Surface area16310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.050, 69.050, 113.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein NEUROPHYSIN II / BNPII


Mass: 9890.252 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: POSTERIOR PITUITARY GLAND / References: UniProt: P01180
#2: Protein/peptide OXYTOCIN / OT


Mass: 1010.188 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
#3: Protein NEUROPHYSIN II / BNPII


Mass: 9832.150 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: POSTERIOR PITUITARY GLAND / References: UniProt: P01180

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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: 2.92 Å3/Da / Density % sol: 58 % / Description: DATA WAS COLLECTED IN 2 ORIENTATIONS.
Crystal growpH: 6.8 / Details: pH 6.8
Crystal grow
*PLUS
Temperature: 18 K / pH: 6 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
112.5 mg/mlNP11
20.2 %(w/v)sodium azide11
3OT acetate salt111.7mg
4ammonium sulfate11saturated, 0.02ml per well

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR / Date: Jun 6, 1990 / Details: SUPPER MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 3 Å / Num. obs: 5924 / % possible obs: 99.99 % / Redundancy: 6.4 % / Biso Wilson estimate: 29.17 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 10.6
Reflection shellResolution: 3→3.18 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.253 / Mean I/σ(I) obs: 1.7 / % possible all: 100
Reflection
*PLUS
Num. all: 5928 / Num. measured all: 38324

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Processing

Software
NameVersionClassification
XENGEN2data collection
X-PLOR3.1model building
X-PLOR3.1refinement
XENGENV. 2.0data reduction
X-PLOR3.1phasing
RefinementResolution: 3→8 Å / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.266 527 9.79 %RANDOM
Rwork0.182 ---
obs0.182 5382 96.9 %-
Displacement parametersBiso mean: 30.13 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1513 0 0 0 1513
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.56
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.79
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 3→3.12 Å
RfactorNum. reflection% reflection
Rwork0.228 559 -
obs--94 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARCSDX.PROTOPCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.79

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