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- PDB-1gka: The molecular basis of the coloration mechanism in lobster shell.... -

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Basic information

Entry
Database: PDB / ID: 1gka
TitleThe molecular basis of the coloration mechanism in lobster shell. beta-crustacyanin at 3.2 A resolution
Components(CRUSTACYANIN ...) x 2
KeywordsLIPOCALIN / CRUSTACYANIN / LOBSTER / ASTAXANTHIN / BATHOCHROMIC / COLORATION
Function / homologyLipocalin/cytosolic fatty-acid binding domain / Invertebrate colouration protein / Calycin / Lipocalin, ApoD type / Lipocalin family conserved site / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin signature. / pigment binding / protein-chromophore linkage / extracellular space ...Lipocalin/cytosolic fatty-acid binding domain / Invertebrate colouration protein / Calycin / Lipocalin, ApoD type / Lipocalin family conserved site / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin signature. / pigment binding / protein-chromophore linkage / extracellular space / Crustacyanin-A1 subunit / Crustacyanin-A2 subunit
Function and homology information
Specimen sourceHOMARUS GAMMARUS (European lobster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.23 Å
AuthorsCianci, M. / Rizkallah, P.J. / Olczak, A. / Raftery, J. / Chayen, N.E. / Zagalsky, P.F. / Helliwell, J.R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: The Molecular Basis of the Coloration Mechanism in Lobster Shell: Beta -Crustacyanin at 3.2-A Resolution
Authors: Cianci, M. / Rizkallah, P. / Olczak, A. / Raftery, J. / Chayen, N. / Zagalsky, P. / Helliwell, J.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 10, 2001 / Release: Aug 8, 2002
RevisionDateData content typeGroupProviderType
1.0Aug 8, 2002Structure modelrepositoryInitial release
1.1May 8, 2011Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. REMARK 900

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CRUSTACYANIN A1 SUBUNIT
B: CRUSTACYANIN A2 SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9717
Polyers40,2472
Non-polymers1,7245
Water54030
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
γ
α
β
Length a, b, c (Å)155.466, 155.466, 168.504
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP 63 2 2

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Components

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CRUSTACYANIN ... , 2 types, 2 molecules AB

#1: Protein/peptide CRUSTACYANIN A1 SUBUNIT / BETA CRUSTACYANIN SUBUNIT


Mass: 20558.029 Da / Num. of mol.: 1 / Source: (natural) HOMARUS GAMMARUS (European lobster) / Tissue: CARAPACE / References: UniProt: P58989*PLUS
#2: Protein/peptide CRUSTACYANIN A2 SUBUNIT


Mass: 19688.822 Da / Num. of mol.: 1 / Source: (natural) HOMARUS GAMMARUS (European lobster) / Tissue: CARAPACE / References: UniProt: P80007

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Non-polymers , 5 types, 35 molecules

#3: Chemical ChemComp-AXT / ASTAXANTHIN / 3,3'-DIHYDROXY-BETA,BETA-CAROTENE-4,4'-DIONE


Mass: 596.838 Da / Num. of mol.: 2 / Formula: C40H52O4 / Astaxanthin
#4: Chemical ChemComp-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 1 / Formula: C12H26 / Dodecane
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Formula: C4H12NO3 / Tris / Comment: pH buffer *YM
#6: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Formula: C8H18N2O4S / HEPES / Comment: pH buffer *YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Formula: H2O / Water

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Details

Compound detailsTHIS BETA CRUSTACYANIN IS RESPONSIBLE FOR BINDING THE CAROTENOID ASTAXANTHIN THAT PROVIDES THE ...THIS BETA CRUSTACYANIN IS RESPONSIBLE FOR BINDING THE CAROTENOID ASTAXANTHIN THAT PROVIDES THE COLORATION OF THE CARAPACE OF 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: 7.3 Å3/Da / Density % sol: 78.89 %
Crystal growpH: 7.7 / Details: pH 7.70
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8 / Method: vapor diffusion
components of the solutions
*PLUS

Crystal-ID: 1

IDConc.Common nameSol-IDDetails
110 mg/mlproteindrop
210 mMTris-HCldroppH8.0
31.25 Msodium potassium phosphatereservoirpH7.
40.05 MHEPESreservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488
DetectorDate: Nov 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 3→100 Å / Num. obs: 24504 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 15.5
Reflection shellResolution: 3.23→3.38 Å / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 5.5 / % possible all: 100
Reflection
*PLUS
Highest resolution: 3 Å / Lowest resolution: 100 Å / Num. measured all: 171943
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.35

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H91
Resolution: 3.23→100 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2515-5 %RANDOM
Rwork0.2133---
obs0.21331982799.7 %-
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 3.23→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28430123302996
Refine LS restraints
Refinement-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.031007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.77747
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.55446
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.52549
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS shellResolution: 3.23→3.35 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.391--
Rwork0.30851845-
obs--0.999 %
Refinement
*PLUS
Lowest resolution: 100 Å / Rfactor Rfree: 0.251 / Rfactor Rwork: 0.213
Refine LS restraints
*PLUS
Refinement-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.031
X-RAY DIFFRACTIONc_angle_deg2.78
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.53

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