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- PDB-2bf9: Anisotropic refinement of avian (turkey) pancreatic polypeptide a... -

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Basic information

Entry
Database: PDB / ID: 2bf9
TitleAnisotropic refinement of avian (turkey) pancreatic polypeptide at 0. 99 Angstroms resolution.
ComponentsPANCREATIC HORMONEPancreatic islets
KeywordsHORMONE / PANCREATIC HORMONE / TURKEY / PANCREAS / POLYPEPTIDE / ATOMIC RESOLUTION / ANISOTROPIC REFINEMENT
Function / homologyPancreatic hormone-like / Pancreatic hormone-like, conserved site / Pancreatic hormone peptide / Pancreatic hormone family signature. / Pancreatic hormone family profile. / Pancreatic hormones / neuropeptide F / peptide YY family / hormone activity / extracellular region / Pancreatic polypeptide
Function and homology information
Biological speciesMELEAGRIS GALLOPAVO (turkey)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 0.99 Å
AuthorsTickle, I. / Glover, I. / Pitts, J. / Wood, S. / Blundell, T.L.
Citation
Journal: Biopolymers / Year: 1983
Title: Conformational Flexibility in a Small Globular Hormone. X-Ray Analysis of Avian Pancreatic Polypeptide at 0.98 Angstroms Resolution
Authors: Glover, I. / Haneef, I. / Pitts, J. / Wood, S. / Moss, D. / Tickle, I. / Blundell, T.L.
#1: Journal: Kristallografiya / Year: 1982
Title: Crystal Structure Analysis of Avian Pancreatic Polypeptide at 1.37 Angstroms Resolution
Authors: Pitts, J.E. / Tickle, I.J. / Wood, S.P. / Blundell, T.L.
#2: Journal: Sov.Phys.Crystallogr.(Engl. Transl.) / Year: 1982
Title: Crystal Structure Analysis of Avian Pancreatic Polypeptide at 1.37 Angstroms Resolution
Authors: Pitts, J.E. / Tickle, I.J. / Wood, S.P. / Blundell, T.L.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1981
Title: X-Ray Analysis (1.4-Angstroms Resolution) of Avian Pancreatic Polypeptide. Small Globular Protein Hormone
Authors: Blundell, T.L. / Pitts, J.E. / Tickle, I.J. / Wood, S.P. / Wu, C.-W.
#4: Journal: Eur.J.Biochem. / Year: 1977
Title: Purification, Crystallisation and Preliminary X-Ray Studies on Avian Pancreatic Polypeptide
Authors: Wood, S.P. / Pitts, J.E. / Blundell, T.L. / Tickle, I.J. / Jenkins, J.A.
#5: Journal: J.Biol.Chem. / Year: 1975
Title: Isolation and Characterization of a New Pancreatic Polypeptide Hormone
Authors: Kimmel, J.R. / Hayden, L.J. / Pollock, H.G.
History
DepositionDec 6, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 8, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 22, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status ...pdbx_database_proc / pdbx_database_status / refine / struct_conn
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PANCREATIC HORMONE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,3072
Polymers4,2421
Non-polymers651
Water1,47782
1
A: PANCREATIC HORMONE
hetero molecules

A: PANCREATIC HORMONE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,6144
Polymers8,4832
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
MethodPQS
Unit cell
Length a, b, c (Å)34.180, 32.920, 28.450
Angle α, β, γ (deg.)90.00, 105.26, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2004-

HOH

21A-2032-

HOH

31A-2048-

HOH

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Components

#1: Protein/peptide PANCREATIC HORMONE / Pancreatic islets / AVIAN PANCREATIC POLYPEPTIDE / PP / PANCREATIC POLYPEPTIDE


Mass: 4241.634 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: COLLECTED FROM COMMERCIAL UK TURKEY FARM. / Source: (natural) MELEAGRIS GALLOPAVO (turkey) / Cell: ISLETS OF LANGERHANS / Organ: PANCREAS / References: UniProt: P68249
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 4

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Sample preparation

CrystalDensity Matthews: 1.8 Å3/Da / Density % sol: 31.14 %
Crystal growpH: 7
Details: 5MG/ML POLYPEPTIDE IN 0.1M TRIS-HCL BUFFER, 0.001M ZN(OAC)2, pH 7.00

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SEALED TUBE / Type: HILGER-WATTS 1.2KW / Wavelength: 1.54178
DetectorType: HILGER-WATTS / Detector: Y290 SCINTILLATION COUNTER / Date: Jan 1, 1983 / Details: HELIUM PATH
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 0.99→27.45 Å / Num. obs: 17058 / % possible obs: 94.7 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.06

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Processing

Software
NameVersionClassification
SHELXL-97refinement
ON-LINECENTROID INTEGRATIONdata reduction
HRSdata scaling
CCP4phasing
RefinementMethod to determine structure: SIRAS / Resolution: 0.99→27.45 Å / Num. parameters: 3457 / Num. restraintsaints: 1694 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: THIS IS A REFINEMENT OF PDB ENTRY 1PPT USING NEW X-RAY DATA AT ATOMIC RESOLUTION.
RfactorNum. reflection% reflectionSelection details
Rfree0.1794 852 5 %RANDOM
all0.1371 17058 --
obs0.1368 -94.72 %-
Refine analyzeNum. disordered residues: 1 / Occupancy sum hydrogen: 281 / Occupancy sum non hydrogen: 382.5
Refinement stepCycle: LAST / Resolution: 0.99→27.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms301 0 1 82 384
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d0.026
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0198
X-RAY DIFFRACTIONs_zero_chiral_vol0.093
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.082
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.013
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.007
X-RAY DIFFRACTIONs_similar_adp_cmpnt0
X-RAY DIFFRACTIONs_approx_iso_adps0

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