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- PDB-2i3f: Crystal Structure of a Glycolipid transfer-like protein from Gald... -

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Basic information

Entry
Database: PDB / ID: 2i3f
TitleCrystal Structure of a Glycolipid transfer-like protein from Galdieria sulphuraria
Componentsglycolipid transfer-like protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / GLTP superfamily / GLTP-like / Protein structure initiative / PSI / Center for Eukaryotic Structural Genomics / CESG
Function / homologyGlycolipid transfer protein, GLTP / Glycolipid transfer protein / Orthogonal Bundle / Mainly Alpha
Function and homology information
Biological speciesGaldieria sulphuraria (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsMcCoy, J.G. / Wesenberg, G.E. / Phillips Jr., G.N. / Bitto, E. / Bingman, C.A. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: To be Published
Title: Crystal Structure of a Glycolipid transfer-like protein from Galdieria sulphuraria
Authors: McCoy, J.G. / Wesenberg, G.E. / Phillips Jr., G.N. / Bitto, E. / Bingman, C.A. / Center for Eukaryotic Structural Genomics (CESG)
History
DepositionAug 18, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: glycolipid transfer-like protein
B: glycolipid transfer-like protein


Theoretical massNumber of molelcules
Total (without water)51,7382
Polymers51,7382
Non-polymers00
Water6,918384
1
A: glycolipid transfer-like protein


Theoretical massNumber of molelcules
Total (without water)25,8691
Polymers25,8691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: glycolipid transfer-like protein


Theoretical massNumber of molelcules
Total (without water)25,8691
Polymers25,8691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.438, 48.195, 89.411
Angle α, β, γ (deg.)90.000, 115.060, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-240-

HOH

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Components

#1: Protein glycolipid transfer-like protein


Mass: 25868.814 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Galdieria sulphuraria (eukaryote) / Gene: c503_101305g25.t1 (MSU_Galdi) / Plasmid: PVP 16 / Production host: Escherichia coli (E. coli) / Strain (production host): BL834 P(RARE2)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / 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: 2.2 Å3/Da / Density % sol: 44.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.050 M SODIUM CHLORIDE, 0.0003 M TCEP, 0.005 M Tris PH 8.0) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (16% PEG 1.5K, 0.050 M HEPES pH 7.5) ...Details: PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.050 M SODIUM CHLORIDE, 0.0003 M TCEP, 0.005 M Tris PH 8.0) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (16% PEG 1.5K, 0.050 M HEPES pH 7.5) CRYOPROTECTED WITH WELL SOLUTION WITH 20% glycerol, vapor diffusion, hanging drop, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 22-ID10.97925
2
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 4, 2006
Details: HORIZONTAL SAGITALLY FOCUSING 2ND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR
RadiationMonochromator: CRYOGENICALLY COOLED SI (220) DOUBLE BOUNCE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97925 Å / Relative weight: 1
ReflectionResolution: 1.38→43.963 Å / Num. obs: 93177 / % possible obs: 99.1 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.036 / Χ2: 0.952 / Net I/σ(I): 17.474
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.38-1.432.90.2463.75486350.86392.4
1.43-1.493.40.18392950.87399.5
1.49-1.553.60.13293770.904100
1.55-1.643.70.193440.976100
1.64-1.743.70.08493561.031100
1.74-1.873.70.06193771.016100
1.87-2.063.80.04293950.984100
2.06-2.363.80.04494340.892100
2.36-2.973.80.03494400.879100
2.97-43.9633.70.02895241.06398.8

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation3 Å43.96 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: FFAS03 homology model based on PDB 1tfj

1tfj


Resolution: 1.38→43.963 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.229 / WRfactor Rwork: 0.198 / SU B: 0.903 / SU ML: 0.037 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.058 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.213 4669 5.011 %RANDOM
Rwork0.182 ---
all0.184 ---
obs0.184 93176 99.013 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 19.835 Å2
Baniso -1Baniso -2Baniso -3
1--0.324 Å20 Å20.129 Å2
2--0.427 Å20 Å2
3---0.007 Å2
Refinement stepCycle: LAST / Resolution: 1.38→43.963 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3417 0 0 384 3801
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0223503
X-RAY DIFFRACTIONr_angle_refined_deg1.7811.9534761
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7995434
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.50624.048168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.73615639
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9281524
X-RAY DIFFRACTIONr_chiral_restr0.1120.2538
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022634
X-RAY DIFFRACTIONr_nbd_refined0.2190.21867
X-RAY DIFFRACTIONr_nbtor_refined0.320.22488
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2270
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1510.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1910.221
X-RAY DIFFRACTIONr_mcbond_it1.4151.52170
X-RAY DIFFRACTIONr_mcangle_it2.04923413
X-RAY DIFFRACTIONr_scbond_it2.98431535
X-RAY DIFFRACTIONr_scangle_it4.4534.51338
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.38-1.4160.3093020.2715927692689.936
1.416-1.4550.2763140.2426339676198.403
1.455-1.4970.2543230.2096201653099.908
1.497-1.5430.2293390.19360026341100
1.543-1.5930.2133340.18558536187100
1.593-1.6490.2173010.18957136014100
1.649-1.7110.2112680.18954785746100
1.711-1.7810.2262690.18953215590100
1.781-1.860.2182710.1845042531499.981
1.86-1.9510.2022550.18548565111100
1.951-2.0570.2092310.1846244855100
2.057-2.1810.2272470.17843754622100
2.181-2.3320.192010.1694107430999.977
2.332-2.5180.2262150.17738184033100
2.518-2.7590.2162020.17835273729100
2.759-3.0840.1911660.1823210337999.911
3.084-3.560.21480.182852300399.9
3.56-4.3580.1721300.1582385252999.446
4.358-6.1540.238970.1721881198799.547
6.154-43.9630.24560.21996113992.362

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