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- PDB-1d5c: CRYSTAL STRUCTURE OF PLASMODIUM FALCIPARUM RAB6 COMPLEXED WITH GDP -

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Basic information

Entry
Database: PDB / ID: 1d5c
TitleCRYSTAL STRUCTURE OF PLASMODIUM FALCIPARUM RAB6 COMPLEXED WITH GDP
ComponentsRAB6 GTPASE
KeywordsENDOCYTOSIS/EXOCYTOSIS / G-PROTEIN / GTPASE / RAB / RAB6 / VESICULAR TRAFFICKING / ENDOCYTOSIS-EXOCYTOSIS COMPLEX
Function / homology
Function and homology information


GTPase activity / GTP binding
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 / GTPase (Rab6)
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsChattopadhyay, D. / Langsley, G. / Carson, M. / Recacha, R. / DeLucas, L. / Smith, C.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Structure of the nucleotide-binding domain of Plasmodium falciparum rab6 in the GDP-bound form.
Authors: Chattopadhyay, D. / Langsley, G. / Carson, M. / Recacha, R. / DeLucas, L. / Smith, C.
History
DepositionOct 6, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory / Refinement description
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RAB6 GTPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2053
Polymers18,7381
Non-polymers4682
Water1,13563
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.200, 81.200, 90.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein RAB6 GTPASE


Mass: 18737.814 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Plasmid: PET21 / Production host: Escherichia coli (E. coli) / References: UniProt: Q26000
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 3.9 Å3/Da / Density % sol: 68 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: sodium sulfate, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.0 Msodium sulfate1reservoir
20.1 Msodium cacodylate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Type: APS / Wavelength: 0.9789, 0.9770, 0.9791
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 25, 1999
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97891
20.9771
30.97911
ReflectionResolution: 2.2→20 Å / Num. all: 15971 / Num. obs: 15968 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 18.4 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 25.4
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 18.7 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 12.6 / Num. unique all: 1560 / % possible all: 100
Reflection
*PLUS
Num. measured all: 294170
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.28 Å / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 11.2

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Processing

Software
NameVersionClassification
MAR345data collection
d*TREKdata reduction
SOLVEphasing
CNS0.9refinement
d*TREKdata scaling
RefinementResolution: 2.3→9.94 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1501218.1 / Data cutoff high rms absF: 1501218.1 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: MLF
Details: F48 has been fixed because it lies on a two fold symmetry element.
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1391 10.1 %RANDOM
Rwork0.214 ---
all-13831 --
obs-13776 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.4068 Å2 / ksol: 0.371 e/Å3
Displacement parametersBiso mean: 34.3 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.31 Å
Luzzati d res low-10 Å
Luzzati sigma a0.24 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.3→9.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1311 0 29 63 1403
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_improper_angle_d0.63
X-RAY DIFFRACTIONc_mcbond_it3.441.5
X-RAY DIFFRACTIONc_mcangle_it3.512
X-RAY DIFFRACTIONc_scbond_it1.822
X-RAY DIFFRACTIONc_scangle_it2.842.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.266 234 10.4 %
Rwork0.25 2022 -
obs--99.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAM
X-RAY DIFFRACTION3GDP_F.PARAM
X-RAY DIFFRACTION4WATER_REP.PARA
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
σ(F): 3 / % reflection Rfree: 10.1 % / Rfactor obs: 0.214
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 34.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.63
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.266 / % reflection Rfree: 10.4 % / Rfactor Rwork: 0.25

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