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- PDB-3kv0: Crystal structure of HET-C2: A FUNGAL GLYCOLIPID TRANSFER PROTEIN... -

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Basic information

Entry
Database: PDB / ID: 3kv0
TitleCrystal structure of HET-C2: A FUNGAL GLYCOLIPID TRANSFER PROTEIN (GLTP)
ComponentsHET-C2
KeywordsTRANSPORT PROTEIN / HET-C2 / GLTP / Glycolipid transfer protein
Function / homology
Function and homology information


ceramide 1-phosphate transfer activity / ceramide 1-phosphate binding / membrane / cytosol
Similarity search - Function
Glycolipid transfer protein domain / Glycolipid transfer protein superfamily / Glycolipid transfer protein (GLTP) / Glycolipid transfer protein, GLTP / Glycolipid transfer protein / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesPodospora anserina (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSimanshu, D.K. / Kenoth, R. / Brown, R.E. / Patel, D.J.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structural determination and tryptophan fluorescence of heterokaryon incompatibility C2 protein (HET-C2), a fungal glycolipid transfer protein (GLTP), provide novel insights into glycolipid ...Title: Structural determination and tryptophan fluorescence of heterokaryon incompatibility C2 protein (HET-C2), a fungal glycolipid transfer protein (GLTP), provide novel insights into glycolipid specificity and membrane interaction by the GLTP fold.
Authors: Kenoth, R. / Simanshu, D.K. / Kamlekar, R.K. / Pike, H.M. / Molotkovsky, J.G. / Benson, L.M. / Bergen, H.R. / Prendergast, F.G. / Malinina, L. / Venyaminov, S.Y. / Patel, D.J. / Brown, R.E.
History
DepositionNov 28, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HET-C2


Theoretical massNumber of molelcules
Total (without water)23,7831
Polymers23,7831
Non-polymers00
Water2,126118
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: HET-C2

A: HET-C2


Theoretical massNumber of molelcules
Total (without water)47,5652
Polymers47,5652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area1180 Å2
ΔGint-14 kcal/mol
Surface area19040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.926, 96.926, 57.914
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein HET-C2


Mass: 23782.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Podospora anserina (fungus) / Gene: het-c2 / Plasmid: pET-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q01494
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.86 Å3/Da / Density % sol: 56.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-Tris (pH 5.5-6.5) and 25 % PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
PH range: 5.5-6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 6, 2009
Details: Cryogenically-cooled single crystal Si(111) side bounce monochromator. Optional Si(311) to achive 13.474 keV. Vertical and horizantal focussing mirrors in Kirkpatrick-Baez geometry.
RadiationMonochromator: Cryogenically-cooled single crystal Si(111) side bounce monochromator. Optional Si(311) to achive 13.474 keV
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 22551 / Redundancy: 8.7 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 36.8
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 6 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 2.95 / % possible all: 93.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0070refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: human apo-GLTP (PDB: 1SWX)

1swx


Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.229 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24816 1132 5.1 %RANDOM
Rwork0.21594 ---
obs0.21755 20958 98.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.073 Å2
Baniso -1Baniso -2Baniso -3
1--0.88 Å20 Å20 Å2
2---0.88 Å20 Å2
3---1.77 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1564 0 0 118 1682
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221606
X-RAY DIFFRACTIONr_bond_other_d0.0010.021105
X-RAY DIFFRACTIONr_angle_refined_deg1.5122.022169
X-RAY DIFFRACTIONr_angle_other_deg0.92432700
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9965196
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.9724.05869
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.22215252
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1711510
X-RAY DIFFRACTIONr_chiral_restr0.1010.2256
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021724
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02320
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0191.5973
X-RAY DIFFRACTIONr_mcbond_other0.2191.5391
X-RAY DIFFRACTIONr_mcangle_it1.8621569
X-RAY DIFFRACTIONr_scbond_it2.6533633
X-RAY DIFFRACTIONr_scangle_it4.3874.5598
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 65 -
Rwork0.288 1465 -
obs--93.75 %

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