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- PDB-1i4u: THE C1 SUBUNIT OF ALPHA-CRUSTACYANIN -

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Basic information

Entry
Database: PDB / ID: 1i4u
TitleTHE C1 SUBUNIT OF ALPHA-CRUSTACYANIN
ComponentsCRUSTACYANIN
KeywordsTRANSPORT PROTEIN / Lipocalin fold / antiparallel beta barrel
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
MethodX-RAY DIFFRACTION / SYNCHROTRON / ab initio using S positions from 'anomalous data' collected at 1.77A wavelength / Resolution: 1.15 Å
AuthorsGordon, E.J. / Leonard, G.A. / McSweeney, S. / Zagalsky, P.F.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2001
Title: The C1 subunit of alpha-crustacyanin: the de novo phasing of the crystal structure of a 40 kDa homodimeric protein using the anomalous scattering from S atoms combined with direct methods.
Authors: Gordon, E.J. / Leonard, G.A. / McSweeney, S. / Zagalsky, P.F.
History
DepositionFeb 23, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2001Provider: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CRUSTACYANIN
B: CRUSTACYANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0418
Polymers41,3762
Non-polymers6656
Water7,728429
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-115 kcal/mol
Surface area15870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.230, 79.720, 109.490
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


Mass: 20688.061 Da / Num. of mol.: 2 / Fragment: C1 SUBUNIT / Source method: obtained synthetically
Details: This peptide was chemically synthesized. The sequence of this peptide occurs naturally in Homarus gammarus (European lobster).
References: UniProt: P80029
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 429 / 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: 2.17 Å3/Da / Density % sol: 43.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9
Details: amonium sulphate, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal grow
*PLUS
Details: Wright, C.E., (1992) J. Mol. Biol., 224, 283.

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.77, 0.72
Detector
TypeIDDetectorDate
MARRESEARCH1CCDSep 3, 2000
MARRESEARCH2CCDSep 3, 2000
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1BM14SINGLE WAVELENGTHMx-ray1
2BM14SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.771
20.721
ReflectionResolution: 1.1→40 Å / Num. all: 145492 / Num. obs: 145492 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 24.5
Reflection shellResolution: 1.1→1.12 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.453 / % possible all: 99.1
Reflection
*PLUS

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
SHARPphasing
ACORNphasing
SHELXL-97refinement
RefinementMethod to determine structure: ab initio using S positions from 'anomalous data' collected at 1.77A wavelength
Resolution: 1.15→40 Å / σ(F): 0 / σ(I): 0
Stereochemistry target values: Engh & Huber as implemented in SHELXLL
RfactorNum. reflectionSelection details
Rfree0.188 6420 RANDOM
Rwork0.15 --
all0.15 121722 -
obs0.15 121722 -
Refinement stepCycle: LAST / Resolution: 1.15→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2911 0 10 461 3382
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d2.4
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 40 Å / σ(F): 0 / Rfactor all: 0.15 / Rfactor obs: 0.1496 / Rfactor Rwork: 0.15
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2.4

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