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- PDB-2q52: Ensemble refinement of the crystal structure of a glycolipid tran... -

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Basic information

Entry
Database: PDB / ID: 2q52
TitleEnsemble refinement of the crystal structure of a glycolipid transfer-like protein from Galdieria sulphuraria
ComponentsGlycolipid transfer-like protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Ensemble Refinement / Refinement Methodology Development / 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 / Re-refinement using ensemble model / Resolution: 1.38 Å
AuthorsLevin, E.J. / Kondrashov, D.A. / Wesenberg, G.E. / Phillips Jr., G.N. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: Structure / Year: 2007
Title: Ensemble refinement of protein crystal structures: validation and application.
Authors: Levin, E.J. / Kondrashov, D.A. / Wesenberg, G.E. / Phillips, G.N.
History
DepositionMay 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 10, 2011Group: Other
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
Remark 999 SEQUENCE THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT DATABASE AT THE TIME OF DEPOSITION.

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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
Number of models8
Components on special symmetry positions
IDModelComponents
11B-241-

HOH

22B-240-

HOH

33B-239-

HOH

44B-241-

HOH

55B-240-

HOH

66B-239-

HOH

77B-240-

HOH

88B-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: PVP16 / 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

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.6 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 2I3F.

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT2data extraction
CNS1.1phasing
RefinementMethod to determine structure: Re-refinement using ensemble model
Starting model: PDB entry 2I3F

2i3f


Resolution: 1.38→41.99 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2180669.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: maximum likelihood using amplitudes
Details: This PDB entry is a re-refinement using an ensemble model of the previously deposited single-conformer structure 2i3f and the first data set in the deposited structure factor file for 2i3f ...Details: This PDB entry is a re-refinement using an ensemble model of the previously deposited single-conformer structure 2i3f and the first data set in the deposited structure factor file for 2i3f along with the R-free set defined therein. The coordinates were generated by an automated protocol from an initial model consisting of 8 identical copies of the protein and non-water hetero-atoms assigned fractional occupancies adding up to one, and a single copy of the solvent molecules. Refinement was carried out with all the conformers present simultaneously and with the potential energy terms corresponding to interactions between the different conformers excluded. The helix and sheet records were calculated using coordinates from the first conformer only. The structure visualization program PYMOL is well-suited for directly viewing the ensemble model presented in this PDB file.
RfactorNum. reflection% reflectionSelection details
Rfree0.202 4669 5 %RANDOM
Rwork0.166 ---
obs0.166 93170 98.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.95 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 16.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å20 Å21.04 Å2
2---0.25 Å20 Å2
3---0.91 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.15 Å0.12 Å
Luzzati d res low-5 Å
Luzzati sigma a0.06 Å-0.02 Å
Refinement stepCycle: LAST / Resolution: 1.38→41.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3348 0 0 384 3732
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d19.3
X-RAY DIFFRACTIONc_improper_angle_d1.24
X-RAY DIFFRACTIONc_mcbond_it1.341.5
X-RAY DIFFRACTIONc_mcangle_it1.742
X-RAY DIFFRACTIONc_scbond_it2.242
X-RAY DIFFRACTIONc_scangle_it3.112.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
1.38-1.470.2646984.70.224140620.01156191476094.5
1.47-1.580.1778305.30.136147520.006156131558299.8
1.58-1.740.1727614.90.126148750.006156521563699.9
1.74-1.990.19478150.151148930.007156841567499.9
1.99-2.510.20379050.16148630.007156621565399.9
2.51-41.980.2068095.10.179150560.007159781586599.3
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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