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- PDB-3clv: Crystal Structure of Rab5a from plasmodium falciparum, PFB0500c -

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Basic information

Entry
Database: PDB / ID: 3clv
TitleCrystal Structure of Rab5a from plasmodium falciparum, PFB0500c
ComponentsRab5 protein, putative
KeywordsSIGNALING PROTEIN / malaria / gtpase / Rab / structural genomics / GTP-binding / Nucleotide-binding / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / regulation of vacuole fusion, non-autophagic / Neutrophil degranulation / small GTPase-mediated signal transduction / endocytic vesicle / endomembrane system / small monomeric GTPase / intracellular protein transport / endosome ...RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / regulation of vacuole fusion, non-autophagic / Neutrophil degranulation / small GTPase-mediated signal transduction / endocytic vesicle / endomembrane system / small monomeric GTPase / intracellular protein transport / endosome / GTPase activity / GTP binding
Similarity search - Function
Ras of Complex, Roc, domain of DAPkinase / 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-5A
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.89 Å
AuthorsChattopadhyay, D. / Wernimont, A.K. / Langsley, G. / Lew, J. / Kozieradzki, I. / Cossar, D. / Schapira, M. / Bochkarev, A. / Arrowsmith, C.H. / Bountra, C. ...Chattopadhyay, D. / Wernimont, A.K. / Langsley, G. / Lew, J. / Kozieradzki, I. / Cossar, D. / Schapira, M. / Bochkarev, A. / Arrowsmith, C.H. / Bountra, C. / Weigelt, J. / Edwards, A.M. / Hui, R. / Sukumar, D. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal Structure of Rab5a from plasmodium falciparum, PFB0500c
Authors: Chattopadhyay, D. / Wernimont, A.K. / Langsley, G. / Lew, J. / Kozieradzki, I. / Cossar, D. / Schapira, M. / Bochkarev, A. / Arrowsmith, C.H. / Bountra, C. / Weigelt, J. / Edwards, A.M. / Hui, R. / Sukumar, D.
History
DepositionMar 20, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / 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

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Assembly

Deposited unit
A: Rab5 protein, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1764
Polymers23,6621
Non-polymers5143
Water1,874104
1
A: Rab5 protein, putative
hetero molecules

A: Rab5 protein, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3518
Polymers47,3232
Non-polymers1,0286
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area3620 Å2
ΔGint-57.1 kcal/mol
Surface area16360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.964, 66.964, 76.128
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-286-

HOH

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Components

#1: Protein Rab5 protein, putative


Mass: 23661.584 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: PFB0500c / Plasmid: p15-mhl / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 / References: UniProt: O96193
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#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.: 104 / 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: 2.08 Å3/Da / Density % sol: 40.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG3350, 0.2 M NaH2PO4, 5mM GDP, 15% glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 12, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.89→50 Å / Num. all: 16260 / Num. obs: 15713 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.4 % / Biso Wilson estimate: 23.899 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.044 / Χ2: 1.726 / Net I/σ(I): 15.9
Reflection shellResolution: 1.89→1.96 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 7.8 / Num. unique all: 1568 / Rsym value: 0.42 / Χ2: 1.804 / % possible all: 98.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å33.48 Å
Translation2.5 Å33.48 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→33.48 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.903 / SU B: 3.449 / SU ML: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.167 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.252 790 5.1 %RANDOM
Rwork0.204 ---
all0.206 16175 --
obs0.206 15587 96.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.551 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.89→33.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1398 0 30 104 1532
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221451
X-RAY DIFFRACTIONr_angle_refined_deg1.3141.9681976
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.475178
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.99225.69265
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.73915254
X-RAY DIFFRACTIONr_dihedral_angle_4_deg4.664154
X-RAY DIFFRACTIONr_chiral_restr0.0930.2234
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021055
X-RAY DIFFRACTIONr_nbd_refined0.1950.2615
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21004
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2102
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2240.215
X-RAY DIFFRACTIONr_mcbond_it0.7871.5905
X-RAY DIFFRACTIONr_mcangle_it1.34621423
X-RAY DIFFRACTIONr_scbond_it1.8593646
X-RAY DIFFRACTIONr_scangle_it2.6764.5550
LS refinement shellResolution: 1.894→1.943 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.432 43 -
Rwork0.296 1117 -
all-1160 -
obs-1568 98.56 %

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