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- PDB-3bfk: Crystal structure of Plasmodium falciparum Rab11a in complex with GDP -

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Basic information

Entry
Database: PDB / ID: 3bfk
TitleCrystal structure of Plasmodium falciparum Rab11a in complex with GDP
ComponentsSmall GTPase Rab11
KeywordsHYDROLASE / Malaria / Rab / GTPase / Structural Genomics Consortium / SGC / GTP-binding / Nucleotide-binding
Function / homology
Function and homology information


RAB geranylgeranylation / rhoptry / small GTPase-mediated signal transduction / small monomeric GTPase / recycling endosome / endosome / GTPase activity / GTP binding / cytosol
Similarity search - Function
Small GTPase / Ras family / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Ras-related protein Rab-11A
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsPizarro, J.C. / Sukumar, D. / Hassanali, A. / Lin, L. / Wernimont, A.K. / Lew, J. / Kozieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. ...Pizarro, J.C. / Sukumar, D. / Hassanali, A. / Lin, L. / Wernimont, A.K. / Lew, J. / Kozieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Sundstrom, M. / Bochkarev, A. / Hui, R. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of Plasmodium falciparum Rab11a in complex with GDP.
Authors: Pizarro, J.C. / Sukumar, D. / Hassanali, A. / Lin, L. / Wernimont, A.K. / Lew, J. / Kozieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Sundstrom, M. / Bochkarev, A. / Hui, R.
History
DepositionNov 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Small GTPase Rab11
B: Small GTPase Rab11
C: Small GTPase Rab11
D: Small GTPase Rab11
E: Small GTPase Rab11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,93513
Polymers103,4425
Non-polymers2,4928
Water7,746430
1
A: Small GTPase Rab11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1322
Polymers20,6881
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Small GTPase Rab11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3164
Polymers20,6881
Non-polymers6273
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Small GTPase Rab11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2243
Polymers20,6881
Non-polymers5352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Small GTPase Rab11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1322
Polymers20,6881
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Small GTPase Rab11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1322
Polymers20,6881
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.490, 48.371, 119.236
Angle α, β, γ (deg.)90.000, 92.360, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Small GTPase Rab11


Mass: 20688.467 Da / Num. of mol.: 5 / Fragment: Residues 6-185
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Gene: PF13_0119 / Plasmid: pET15-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rossetta Oxford / References: UniProt: Q76NM4, small monomeric GTPase
#2: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 430 / 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: 2.33 Å3/Da / Density % sol: 47.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.9
Details: 26% PEG 4000, 100mM Na Citrate, 200mM NH4 Acetate, pH 5.9, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 6, 2007 / Details: Rh-coated Si mirror for vertical focusing
RadiationMonochromator: Bent triangular asymmetric cut Si(111) for horizontal focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. obs: 91227 / % possible obs: 97.9 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.183 / Χ2: 1.184 / Net I/σ(I): 4.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.77-1.832.80.80183680.585190.5
1.83-1.913.30.70990140.657197.6
1.91-1.993.40.49290880.801198.1
1.99-2.13.40.34691291.035198.2
2.1-2.233.30.27590991.198198.5
2.23-2.43.40.23591781.399198.7
2.4-2.643.40.21392201.482199
2.64-3.033.30.18292681.518199.1
3.03-3.813.30.15993101.537199.4
3.81-503.20.14895531.42199.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1OIV

1oiv


Resolution: 1.8→19.95 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.916 / SU B: 3.408 / SU ML: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.151 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.259 4367 5 %RANDOM
Rwork0.218 ---
obs0.22 87258 98.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.274 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å2-0.07 Å2
2--0.09 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6620 0 158 430 7208
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0227192
X-RAY DIFFRACTIONr_bond_other_d0.0020.024820
X-RAY DIFFRACTIONr_angle_refined_deg1.3421.989789
X-RAY DIFFRACTIONr_angle_other_deg0.977311830
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5635898
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.24825.14358
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.992151335
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3311538
X-RAY DIFFRACTIONr_chiral_restr0.0810.21114
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027900
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021456
X-RAY DIFFRACTIONr_nbd_refined0.2060.21193
X-RAY DIFFRACTIONr_nbd_other0.1940.24468
X-RAY DIFFRACTIONr_nbtor_refined0.1710.23247
X-RAY DIFFRACTIONr_nbtor_other0.0790.23488
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2281
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2220.229
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1930.272
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.280.227
X-RAY DIFFRACTIONr_mcbond_it0.8211.54388
X-RAY DIFFRACTIONr_mcbond_other0.1651.51729
X-RAY DIFFRACTIONr_mcangle_it1.30926806
X-RAY DIFFRACTIONr_scbond_it1.70733313
X-RAY DIFFRACTIONr_scangle_it2.64.52936
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 279 -
Rwork0.327 5772 -
all-6051 -
obs--93.86 %

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