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- PDB-2bn2: CRYSTAL STRUCTURE OF BOVINE NEUROPHYSIN II COMPLEXED WITH THE VAS... -

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Basic information

Entry
Database: PDB / ID: 2bn2
TitleCRYSTAL STRUCTURE OF BOVINE NEUROPHYSIN II COMPLEXED WITH THE VASOPRESSIN ANALOGUE PHE-TYR AMIDE
ComponentsNEUROPHYSIN II
KeywordsHORMONE / HORMONE PACKAGING / TRANSPORT / PROTEIN-PEPTIDE 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
PHENYLALANINE / TYROSINE / Vasopressin-neurophysin 2-copeptin
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SAS / Resolution: 2.8 Å
AuthorsRose, J.P. / Wang, B.C.
Citation
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.
#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: 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
DepositionDec 18, 1998Processing site: BNL
SupersessionFeb 16, 1999ID: 1BN2
Revision 1.0Feb 16, 1999Provider: 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 ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
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_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 650 HELIX DETERMINATION METHOD: KSDSSP
Remark 700 SHEET DETERMINATION METHOD: KSDSSP

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NEUROPHYSIN II
C: NEUROPHYSIN II
E: NEUROPHYSIN II
G: NEUROPHYSIN II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,94712
Polymers39,5614
Non-polymers1,3868
Water00
1
A: NEUROPHYSIN II
C: NEUROPHYSIN II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4736
Polymers19,7812
Non-polymers6934
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-6 kcal/mol
Surface area8560 Å2
MethodPISA
2
E: NEUROPHYSIN II
G: NEUROPHYSIN II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4736
Polymers19,7812
Non-polymers6934
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-7 kcal/mol
Surface area7780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.670, 67.960, 62.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.482, 0.672, 0.571), (0.665, -0.137, 0.734), (0.571, 0.727, -0.381)85.457, -13.489, -62.477
2given(-0.875, -0.035, 0.483), (0.003, -0.998, -0.066), (0.484, -0.056, 0.873)48.179, 61.021, -10.337
3given(-0.815, 0.49, -0.309), (0.495, 0.314, -0.81), (-0.3, -0.813, -0.499)60.831, -12.774, 15.613
4given(-0.81, 0.509, -0.291), (0.507, 0.358, -0.784), (-0.295, -0.783, -0.548)60.407, -13.869, 13.694

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Components

#1: Protein
NEUROPHYSIN II / BNPII


Mass: 9890.252 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: POSTERIOR PITUITARY / References: UniProt: P01180
#2: Chemical
ChemComp-PHE / PHENYLALANINE


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H11NO2
#3: Chemical
ChemComp-TYR / TYROSINE


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H11NO3
Has protein modificationY
Nonpolymer detailsRESIDUES 98 AND 99 WITH CHAIN IDS A, C, E AND G FORM THE PHENYLALANINE-TYROSINE AMIDE DIPEPTIDE ...RESIDUES 98 AND 99 WITH CHAIN IDS A, C, E AND G FORM THE PHENYLALANINE-TYROSINE AMIDE DIPEPTIDE (VAL-LYS) WAS BOUND IN THE HORMONE (VASOPRESSIN) BINDING SITE.

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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: 2.82 Å3/Da / Density % sol: 56 %
Description: SAS DATA WERE COLLECTED IN-HOUSE. THE ANOMALOUS SCATTERER WAS PARA IODO-PHENYLALANINE-TYROSINE AMIDE WHICH WAS BOUND IN THE HORMONE BINDING SITE.
Crystal growpH: 6.8
Details: 5 MG OF PROTEIN WAS DISSOLVED IN 0.5 ML OF WATER, 0.5 MG OF PHENYLALANINE-TYROSINE AMIDE AND 20 MICRO LITERS OF SATURATED AMMONIUM SULPHATE SOLUTION WERE ADDED. THE PH OF THE SOLUTION WAS ADJUSTED TO 6.8
Crystal grow
*PLUS
pH: 7.5 / Method: unknown
Components of the solutions
*PLUS
Common name: ammonium sulfate

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Data collection

DiffractionMean temperature: 289 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Sep 13, 1989 / 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: 2.64 Å / Num. obs: 24898 / % possible obs: 83.6 % / Observed criterion σ(I): -3 / Redundancy: 17 % / Biso Wilson estimate: 60.2 Å2 / Rsym value: 0.0404 / Net I/σ(I): 17.05
Reflection shellResolution: 2.64→2.74 Å / Mean I/σ(I) obs: 3.12 / Rsym value: 0.1799 / % possible all: 43.45
Reflection
*PLUS
Highest resolution: 2.8 Å / Num. obs: 12840 / Num. measured all: 58983 / Rmerge(I) obs: 0.0577

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Processing

Software
NameVersionClassification
XENGENdata collection
XENGENdata reduction
ISASmodel building
X-PLOR3.843refinement
XENGENdata scaling
ISASphasing
RefinementMethod to determine structure: SAS / Resolution: 2.8→8 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1207 10.4 %RANDOM
Rwork0.208 ---
obs0.208 11589 92 %-
Displacement parametersBiso mean: 23.7 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2232 0 92 0 2324
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.94
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: 2.8→2.97 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.321 177 11 %
Rwork0.298 1435 -
obs--76.9 %
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 10729 / Rfactor obs: 0.225
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.94
LS refinement shell
*PLUS
Rfactor obs: 0.298

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