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- PDB-1gak: CRYSTAL STRUCTURE OF GREEN ABALONE SP18 -

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Basic information

Entry
Database: PDB / ID: 1gak
TitleCRYSTAL STRUCTURE OF GREEN ABALONE SP18
ComponentsFERTILIZATION PROTEIN
KeywordsCELL ADHESION / helical bundle
Function / homology
Function and homology information


single fertilization
Similarity search - Function
Fertilization protein / Egg lysin (Sperm-lysin) / Egg-lysin superfamily / Egg lysin (Sperm-lysin) / Lysin / Prokaryotic membrane lipoprotein lipid attachment site profile. / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHaliotis fulgens (green abalone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.85 Å
AuthorsKresge, N. / Vacquier, V.D. / Stout, C.D.
CitationJournal: Biochemistry / Year: 2001
Title: The crystal structure of a fusagenic sperm protein reveals extreme surface properties.
Authors: Kresge, N. / Vacquier, V.D. / Stout, C.D.
History
DepositionNov 30, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FERTILIZATION PROTEIN


Theoretical massNumber of molelcules
Total (without water)16,9551
Polymers16,9551
Non-polymers00
Water2,558142
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.760, 68.760, 67.710
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein FERTILIZATION PROTEIN / SP18


Mass: 16954.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haliotis fulgens (green abalone) / Cell: SPERM / References: UniProt: Q25063
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.72 Å3/Da / Density % sol: 54.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 3
Details: mPEG 5000, Ammonium Acetate, Sodium Phosphate, pH 3, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 4.9
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
150 mMsodium acetate1drop
210 mg/mlprotein1drop
325 %mPEG50001reservoir
4200 mMammonium acetate1reservoir
5100 mMsodium phosphate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.77 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 14, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.77 Å / Relative weight: 1
ReflectionResolution: 1.85→59.76 Å / Num. all: 15134 / Num. obs: 15134 / % possible obs: 98.9 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Biso Wilson estimate: 29.35 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 8
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 4 % / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 2.4 / % possible all: 98.9
Reflection
*PLUS
Num. measured all: 82274
Reflection shell
*PLUS
% possible obs: 98.9 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
CNS0.9refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MIR / Resolution: 1.85→60 Å / Isotropic thermal model: isotropic / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2473 828 5.3 %Random
Rwork0.227 ---
all-15596 --
obs-15278 98 %-
Displacement parametersBiso mean: 26.5 Å2
Refinement stepCycle: LAST / Resolution: 1.85→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1151 0 0 142 1293
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009995
X-RAY DIFFRACTIONc_angle_deg1.24185
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 60 Å / σ(F): 0 / % reflection Rfree: 5.3 % / Rfactor obs: 0.227
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 26.5 Å2

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