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- PDB-1z24: The molecular structure of insecticyanin from the tobacco hornwor... -

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Basic information

Entry
Database: PDB / ID: 1z24
TitleThe molecular structure of insecticyanin from the tobacco hornworm Manduca sexta L. at 2.6 A resolution.
ComponentsInsecticyanin A form
KeywordsLIPID BINDING PROTEIN / Blue biliprotein / INS-a / Chromophore binding.
Function / homology
Function and homology information


pigment binding / : / extracellular region
Similarity search - Function
Invertebrate colouration protein / Lipocalin, ApoD type / Lipocalin family conserved site / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
BILIVERDIN IX GAMMA CHROMOPHORE / Insecticyanin-A
Similarity search - Component
Biological speciesManduca sexta (tobacco hornworm)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.6 Å
AuthorsHolden, H.M. / Rypniewski, W.R. / Law, J.H. / Rayment, I.
Citation
Journal: Embo J. / Year: 1987
Title: The molecular structure of insecticyanin from the tobacco hornworm Manduca sexta L. at 2.6 A resolution.
Authors: Holden, H.M. / Rypniewski, W.R. / Law, J.H. / Rayment, I.
#1: Journal: J.Biol.Chem. / Year: 1986
Title: Crystallization of insecticyanin from the hemolymph of the tobacco hornworm Manduca sexta L. in a form suitable for a high resolution structure determination.
Authors: Holden, H.M. / Law, J.H. / Rayment, I.
History
DepositionMar 7, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Insecticyanin A form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9892
Polymers21,4061
Non-polymers5831
Water00
1
A: Insecticyanin A form
hetero molecules

A: Insecticyanin A form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9774
Polymers42,8122
Non-polymers1,1652
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_557y,x,-z+21
Unit cell
Length a, b, c (Å)115.400, 115.400, 71.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Insecticyanin A form / Blue biliprotein / INS-a


Mass: 21406.021 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Manduca sexta (tobacco hornworm) / Keywords: insecticyanin / References: UniProt: P00305
#2: Chemical ChemComp-BLV / BILIVERDIN IX GAMMA CHROMOPHORE


Mass: 582.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H34N4O6

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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: 3.3 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 293 K / Method: batch / pH: 5.5
Details: 20% PEG8000, 100 mM NaCl, 100 mM Nasuccinate, pH 5.5, batch, temperature 293K

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Data collection

DiffractionMean temperature: 278 K
DetectorType: film / Detector: FILM / Date: Jan 1, 1986
RadiationMonochromator: pinhole / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 14167 / Num. obs: 14167 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
APROGRAM BY M. ROSSMAN (ORIGINAL VERSION)data scaling
HEAVYphasing
RefinementMethod to determine structure: MIR / Resolution: 2.6→50 Å / Num. reflection all: 14167 / Num. reflection obs: 14167 / σ(F): 0
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1511 0 43 0 1554

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