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- PDB-1hdf: Evolution of the eye lens beta-gamma-crystallin domain fold -

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Basic information

Entry
Database: PDB / ID: 1hdf
TitleEvolution of the eye lens beta-gamma-crystallin domain fold
ComponentsSPHERULIN 3A
KeywordsSTRUCTURAL PROTEIN / CRYSTALLINS / EYE LENS / DOMAIN INTERACTIONS / SPHERULIN 3A / TYROSINE CORNER
Function / homology
Function and homology information


cell-cell adhesion / membrane / cytoplasm
Similarity search - Function
Calcium-dependent cell adhesion molecule, N-terminal / Beta/Gamma crystallin / Crystallins / Gamma-B Crystallin; domain 1 / Crystallins beta and gamma 'Greek key' motif profile. / Beta/gamma crystallins / Beta/gamma crystallin / Gamma-crystallin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesPHYSARUM POLYCEPHALUM (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.35 Å
AuthorsClout, N.J. / Kretschmar, M. / Jaenicke, R. / Slingsby, C.
CitationJournal: Structure / Year: 2001
Title: Crystal Structure of the Calcium-Loaded Spherulin 3A Dimer Sheds Light on the Evolution of the Eye Lens Betagamma-Crystallin Domain Fold
Authors: Clout, N.J. / Kretschmar, M. / Jaenicke, R. / Slingsby, C.
History
DepositionNov 13, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SPHERULIN 3A
B: SPHERULIN 3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6216
Polymers22,4612
Non-polymers1604
Water2,288127
1
A: SPHERULIN 3A
B: SPHERULIN 3A
hetero molecules

A: SPHERULIN 3A
B: SPHERULIN 3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,24212
Polymers44,9214
Non-polymers3218
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
MethodPQS
Unit cell
Length a, b, c (Å)41.350, 41.350, 213.640
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 SPHERULIN 3A


Mass: 11230.338 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PHYSARUM POLYCEPHALUM (eukaryote) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B84(DE3) / References: UniProt: P09353
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A, B ENGINEERED MUTATION ILE94MSE

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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: 2.12 Å3/Da / Density % sol: 42 %
Crystal growpH: 4.6 / Details: pH 4.60
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 mg/mlprotein1drop
20.2 Mcalcium chloride1reservoir
30.2 Msodium acetate1reservoir
420 %(w/v)2-propanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.95, 0.97885, 0.9791
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.951
20.978851
30.97911
ReflectionResolution: 2.35→20 Å / Num. obs: 10284 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 5.56 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 26.4

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Processing

Software
NameClassification
CNSphasing
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: MAD / Resolution: 2.35→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.239 --
obs0.239 10284 96.7 %
Refinement stepCycle: LAST / Resolution: 2.35→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1544 0 4 127 1675
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005998
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_deg1.16218
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
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

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