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- PDB-1jk6: UNCOMPLEXED DES 1-6 BOVINE NEUROPHYSIN -

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Basic information

Entry
Database: PDB / ID: 1jk6
TitleUNCOMPLEXED DES 1-6 BOVINE NEUROPHYSIN
ComponentsNEUROPHYSIN 2
KeywordsNEUROPEPTIDE / NEUROPHYSIN / HORMONE TRANSPORT / HYPOTHALAMUS
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 / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsRose, J.P. / Wang, B.-C.
Citation
Journal: Protein Sci. / Year: 2003
Title: Structures of an Unliganded Neurophysin and its Vasopressin Complex: Implications for Binding and Allosteric Mechanisms
Authors: Wu, C.K. / Hu, B. / Rose, J.P. / Liu, Z.J. / Nguyen, T.L. / Zeng, C. / Breslow, E. / Wang, B.C.
#1: 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.
#2: 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 Jr., W.F. / Sax, M. / Wang, B.C.
#3: 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.
#4: 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
DepositionJul 11, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Aug 16, 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

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Assembly

Deposited unit
A: NEUROPHYSIN 2
C: NEUROPHYSIN 2


Theoretical massNumber of molelcules
Total (without water)18,4872
Polymers18,4872
Non-polymers00
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-8 kcal/mol
Surface area8140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.920, 48.920, 78.520
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein NEUROPHYSIN 2


Mass: 9243.541 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: RESIDUES 1-6 REMOVED BY ENZYMATIC CLEAVAGE / Source: (natural) Bos taurus (cattle) / References: UniProt: P01180
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.93 Å3/Da / Density % sol: 58.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2M SODIUM CHLORIDE, 0.1M MES BUFFER AND 0.05M SODIUM/POTASSIUM PHOSPATE, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 1, 1996 / Details: YALE/MSC
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→999 Å / % possible obs: 100 % / Rmerge(I) obs: 0.042

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Processing

Software
NameVersionClassification
bioteXdata collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.1refinement
bioteXdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BN2

2bn2


Resolution: 2.4→23 Å / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Rfactor% reflectionSelection details
Rfree0.249 5.2 %RANDOM
Rwork0.218 --
all0.218 --
obs0.218 100 %-
Displacement parametersBiso mean: 37.8 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.4→23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1116 0 0 43 1159
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_dihedral_angle_d24.7
X-RAY DIFFRACTIONx_improper_angle_d1.01
Xplor fileSerial no: 1 / Param file: PARCSDX.PRO / Topol file: TOPCSDX.PRO

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