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- PDB-3p1w: Crystal Structure of RAB GDI from Plasmodium Falciparum, PFL2060c -

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Basic information

Entry
Database: PDB / ID: 3p1w
TitleCrystal Structure of RAB GDI from Plasmodium Falciparum, PFL2060c
ComponentsRabGDI protein
KeywordsPROTEIN TRANSPORT / GDI RAB / malaria / Structural Genomics Consortium / SGC / transport / PF10_0345
Function / homology
Function and homology information


RAB GEFs exchange GTP for GDP on RABs / Rab GDP-dissociation inhibitor activity / small GTPase binding => GO:0031267 / Neutrophil degranulation / small GTPase-mediated signal transduction / vesicle-mediated transport / GTPase activator activity / protein transport / cytoplasm
Similarity search - Function
Rab GDI protein / Guanine Nucleotide Dissociation Inhibitor; domain 2 / Guanine Nucleotide Dissociation Inhibitor, domain 2 / GDP dissociation inhibitor / GDP dissociation inhibitor / Guanine Nucleotide Dissociation Inhibitor, domain 1 / Guanine Nucleotide Dissociation Inhibitor; domain 1 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich ...Rab GDI protein / Guanine Nucleotide Dissociation Inhibitor; domain 2 / Guanine Nucleotide Dissociation Inhibitor, domain 2 / GDP dissociation inhibitor / GDP dissociation inhibitor / Guanine Nucleotide Dissociation Inhibitor, domain 1 / Guanine Nucleotide Dissociation Inhibitor; domain 1 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Rab GDP dissociation inhibitor
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsWernimont, A.K. / Neculai, A.M. / Weadge, J. / MacKenzie, F. / Cossar, D. / Tempel, W. / Bochkarev, A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. ...Wernimont, A.K. / Neculai, A.M. / Weadge, J. / MacKenzie, F. / Cossar, D. / Tempel, W. / Bochkarev, A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Langsley, G. / Bosch, J. / Hui, R. / Pizzaro, J.C. / Hutchinson, A. / Structural Genomics Consortium (SGC)
Citation
Journal: To be published
Title: Crystal Structure of RAB GDI from Plasmodium Falciparum, PFL2060c
Authors: Wernimont, A.K. / Neculai, A.M. / Weadge, J. / MacKenzie, F. / Cossar, D. / Tempel, W. / Bochkarev, A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Langsley, G. / Bosch, J. / Hui, R. / ...Authors: Wernimont, A.K. / Neculai, A.M. / Weadge, J. / MacKenzie, F. / Cossar, D. / Tempel, W. / Bochkarev, A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Langsley, G. / Bosch, J. / Hui, R. / Pizzaro, J.C. / Hutchinson, A.
#1: Journal: Mol.Biochem.Parasitol. / Year: 1996
Title: A Plasmodium falciparum homologue of a rab specific GDP dissociation inhibitor.
Authors: Attal, G. / Langsley, G.
History
DepositionSep 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 29, 2014Group: Database references / Structure summary
Revision 1.3Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.4Sep 6, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RabGDI protein


Theoretical massNumber of molelcules
Total (without water)54,3531
Polymers54,3531
Non-polymers00
Water3,873215
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.885, 116.565, 125.916
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein RabGDI protein


Mass: 54353.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: PFL2060c / Plasmid: pet15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8I501
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.73 Å3/Da / Density % sol: 54.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% PEG 3350, 0.1 M Hepes 7.5, 0.2 M NaCl2, 2 mM TCEP, 5% MPD, glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. all: 59119 / Num. obs: 57819 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 25.9 Å2 / Rmerge(I) obs: 0.057 / Χ2: 1.038 / Net I/σ(I): 9.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.76-1.795.90.9891.5723710.85481.3
1.79-1.826.70.9241.8428540.91196.9
1.82-1.867.10.7142.5828380.90697.7
1.86-1.97.10.618328550.92698
1.9-1.947.10.53328680.98598.1
1.94-1.987.10.37628800.99398.3
1.98-2.037.20.30628931.00998.2
2.03-2.097.20.2528831.03898.5
2.09-2.157.20.20828901.06998.7
2.15-2.227.20.15729131.08298.9
2.22-2.37.20.13128821.11498.7
2.3-2.397.30.11429091.06498.9
2.39-2.57.30.09629211.06799.1
2.5-2.637.30.08229571.06999.3
2.63-2.797.40.06429041.03999.1
2.79-3.017.40.05129591.05599.4
3.01-3.317.40.04329461.19199.5
3.31-3.797.30.03729951.4799.6
3.79-4.787.10.02730191.08999.8
4.78-5070.02130820.71198.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 58.69 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å45.88 Å
Translation2.5 Å45.88 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LV0

1lv0


Resolution: 1.85→40.44 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.1992 / WRfactor Rwork: 0.18 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8908 / SU B: 5.216 / SU ML: 0.072 / SU R Cruickshank DPI: 0.1169 / SU Rfree: 0.1072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2006 2571 5.1 %RANDOM
Rwork0.1804 ---
all0.1814 51043 --
obs0.1814 50360 98.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 43.78 Å2 / Biso mean: 34.569 Å2 / Biso min: 6.52 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20 Å20 Å2
2---2.03 Å20 Å2
3---1.41 Å2
Refinement stepCycle: LAST / Resolution: 1.85→40.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3523 0 0 215 3738
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223698
X-RAY DIFFRACTIONr_bond_other_d0.0020.022444
X-RAY DIFFRACTIONr_angle_refined_deg1.2641.9585039
X-RAY DIFFRACTIONr_angle_other_deg0.87236024
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6675461
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.64925.427164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.43515644
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.808157
X-RAY DIFFRACTIONr_chiral_restr0.0770.2568
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214105
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02715
X-RAY DIFFRACTIONr_mcbond_it0.6671.52256
X-RAY DIFFRACTIONr_mcbond_other0.181.5909
X-RAY DIFFRACTIONr_mcangle_it1.19523679
X-RAY DIFFRACTIONr_scbond_it1.79931442
X-RAY DIFFRACTIONr_scangle_it2.9044.51357
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 197 -
Rwork0.259 3439 -
all-3636 -
obs--97.82 %
Refinement TLS params.Method: refined / Origin x: 22.4039 Å / Origin y: 14.5863 Å / Origin z: 44.0026 Å
111213212223313233
T0.0697 Å20.0521 Å2-0.0073 Å2-0.0721 Å2-0.0064 Å2--0.0317 Å2
L1.5942 °2-0.5137 °2-0.1015 °2-1.495 °20.4588 °2--1.0229 °2
S0.1329 Å °0.3067 Å °-0.0218 Å °-0.1596 Å °-0.1369 Å °0.074 Å °-0.0253 Å °-0.049 Å °0.004 Å °

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