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- PDB-1obu: Apocrustacyanin C1 crystals grown in space and earth using vapour... -

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Basic information

Entry
Database: PDB / ID: 1obu
TitleApocrustacyanin C1 crystals grown in space and earth using vapour diffusion geometry
ComponentsCRUSTACYANIN C1 SUBUNIT
KeywordsTRANSPORT PROTEIN / LIPOCALIN / ANTIPARALLEL BETA-STRANDS / PIGMENT
Function / homology
Function and homology information


pigment binding / cholesterol binding / response to reactive oxygen species / lipid metabolic process / extracellular region / cytoplasm
Similarity search - Function
Invertebrate colouration protein / Lipocalin, ApoD type / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Crustacyanin-C1 subunit
Similarity search - Component
Biological speciesHOMARUS GAMMARUS (European lobster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2 Å
AuthorsHabash, J. / Boggon, T.J. / Raftery, J. / Chayen, N.E. / Zagalsky, P.F. / Helliwell, J.R.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Apocrustacyanin C(1) Crystals Grown in Space and on Earth Using Vapour-Diffusion Geometry: Protein Structure Refinements and Electron-Density Map Comparisons
Authors: Habash, J. / Boggon, T.J. / Raftery, J. / Chayen, N.E. / Zagalsky, P.F. / Helliwell, J.R.
History
DepositionJan 31, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CRUSTACYANIN C1 SUBUNIT
B: CRUSTACYANIN C1 SUBUNIT


Theoretical massNumber of molelcules
Total (without water)41,3762
Polymers41,3762
Non-polymers00
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)42.018, 81.033, 110.507
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CRUSTACYANIN C1 SUBUNIT


Mass: 20688.061 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) HOMARUS GAMMARUS (European lobster) / References: UniProt: P80029
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O
Compound detailsBINDS A CAROTENOID ASTAXANTHIN, WHICH PROVIDES THE BLUE CARAPACE COLORATION IN THE LOBSTER.

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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: 2.27 Å3/Da / Density % sol: 45.9 %
Crystal growpH: 9 / Details: AMMONIUM SULPHATE, pH 9.00
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion
Details: Snell, E.H., (1997) Acta Crystallogr.,Sect.D, 53, 231.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
20.1 MTris-HCl1drop
31 mMEDTA1droppH7.0
45 %(v/v)MPD1reservoir
51 mMEDTA1reservoir
60.1 MTris-HCl1reservoirpH9.0
71.9 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.7513
DetectorType: MARRESEARCH / Detector: CCD
RadiationMonochromator: BM14 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7513 Å / Relative weight: 1
ReflectionResolution: 2→65.94 Å / Num. obs: 26054 / % possible obs: 99.2 %
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 65.94 Å

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 2→65.94 Å / SU B: 5.6 / SU ML: 0.159 / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.163
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1326 5.1 %RANDOM
Rwork0.174 ---
obs0.177 24728 99.19 %-
Displacement parametersBiso mean: 19 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20 Å20 Å2
2--0.23 Å20 Å2
3----0.77 Å2
Refinement stepCycle: LAST / Resolution: 2→65.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2913 0 0 146 3059
Refinement
*PLUS
Highest resolution: 2 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.034
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg2.5
X-RAY DIFFRACTIONdihedral_angle_d
X-RAY DIFFRACTIONdihedral_angle_deg5.7

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