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- PDB-2wwx: Crystal structure of the SidM/DrrA(GEF/GDF domain)-Rab1(GTPase do... -

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Basic information

Entry
Database: PDB / ID: 2wwx
TitleCrystal structure of the SidM/DrrA(GEF/GDF domain)-Rab1(GTPase domain) complex
Components
  • DRRA
  • RAS-RELATED PROTEIN RAB-1
KeywordsPROTEIN TRANSPORT / GOLGI APPARATUS / ER-GOLGI TRANSPORT / ENDOPLASMIC RETICULUM / PRENYLATION / LIPOPROTEIN / NUCLEOTIDE-BINDING
Function / homology
Function and homology information


: / protein guanylylation / positive regulation of glycoprotein metabolic process / growth hormone secretion / AMPylase activity / protein adenylylation / protein adenylyltransferase / COPII-coated vesicle cargo loading / melanosome transport / vesicle transport along microtubule ...: / protein guanylylation / positive regulation of glycoprotein metabolic process / growth hormone secretion / AMPylase activity / protein adenylylation / protein adenylyltransferase / COPII-coated vesicle cargo loading / melanosome transport / vesicle transport along microtubule / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / host cell cytoplasmic vesicle / Golgi Cisternae Pericentriolar Stack Reorganization / phosphatidylinositol-4-phosphate binding / protein targeting to membrane / COPII-mediated vesicle transport / regulation of GTPase activity / COPI-dependent Golgi-to-ER retrograde traffic / transport vesicle membrane / virion assembly / Golgi organization / autophagosome assembly / endoplasmic reticulum to Golgi vesicle-mediated transport / COPI-mediated anterograde transport / vesicle-mediated transport / endomembrane system / substrate adhesion-dependent cell spreading / guanyl-nucleotide exchange factor activity / small monomeric GTPase / positive regulation of interleukin-8 production / intracellular protein transport / small GTPase binding / autophagy / host cell cytoplasmic vesicle membrane / endocytosis / cell migration / protein guanylyltransferase activity / melanosome / G protein activity / early endosome / defense response to bacterium / cadherin binding / Golgi membrane / GTPase activity / GTP binding / Golgi apparatus / endoplasmic reticulum / extracellular exosome / extracellular region / ATP binding / membrane / cytosol
Similarity search - Function
Ferritin - #70 / DrrA guanine nucleotide-exchange factor domain / : / : / SidM, Rab1-activation domain / SidM, N-terminal domain / DrrA phosphatidylinositol 4-phosphate binding domain / DrrA, PI4P binding domain superfamily / DrrA phosphatidylinositol 4-phosphate binding domain / : ...Ferritin - #70 / DrrA guanine nucleotide-exchange factor domain / : / : / SidM, Rab1-activation domain / SidM, N-terminal domain / DrrA phosphatidylinositol 4-phosphate binding domain / DrrA, PI4P binding domain superfamily / DrrA phosphatidylinositol 4-phosphate binding domain / : / ARF-like small GTPases; ARF, ADP-ribosylation factor / small GTPase Rab1 family profile. / Ferritin / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Ras-related protein Rab-1A / Multifunctional virulence effector protein DrrA / Multifunctional virulence effector protein DrrA
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
LEGIONELLA PNEUMOPHILA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.5 Å
AuthorsSuh, H.Y. / Lee, D.W. / Woo, J.S. / Oh, B.H.
CitationJournal: Embo J. / Year: 2010
Title: Structural Insights Into the Dual Nucleotide Exchange and Gdi Displacement Activity of Sidm/Drra
Authors: Suh, H.Y. / Lee, D.W. / Lee, K.H. / Ku, B. / Choi, S.J. / Woo, J.S. / Kim, Y.G. / Oh, B.H.
History
DepositionOct 30, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2015Group: Data collection / Version format compliance
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RAS-RELATED PROTEIN RAB-1
B: DRRA


Theoretical massNumber of molelcules
Total (without water)44,1692
Polymers44,1692
Non-polymers00
Water2,108117
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-13.4 kcal/mol
Surface area17020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.880, 73.803, 73.665
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein RAS-RELATED PROTEIN RAB-1 / YPT1-RELATED PROTEIN


Mass: 19875.605 Da / Num. of mol.: 1 / Fragment: GTPASE DOMAIN, RESIDUES 4-178 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62820
#2: Protein DRRA / SIDM


Mass: 24293.809 Da / Num. of mol.: 1 / Fragment: RESIDUES 317-533
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LEGIONELLA PNEUMOPHILA (bacteria) / Strain: PHILADELPHIA1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q29ST3, UniProt: Q5ZSQ3*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASN 124 TO ILE
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.28 % / Description: NONE

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. obs: 56689 / % possible obs: 98.3 % / Observed criterion σ(I): 1 / Redundancy: 10.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 59.7
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 13.9 / % possible all: 96.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 1.5→30 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.933 / SU B: 1.187 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.231 3034 5.1 %RANDOM
Rwork0.21164 ---
obs0.21265 56689 98.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.678 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20 Å20 Å2
2---0.25 Å20 Å2
3----0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2921 0 0 117 3038
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222969
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1341.9674004
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.335367
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.5325.231130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.08815565
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8331513
X-RAY DIFFRACTIONr_chiral_restr0.0740.2456
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022174
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.210.21321
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.22082
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0960.2123
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2160.236
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1070.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.761.51878
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.27522960
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.13631229
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2734.51044
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 208 -
Rwork0.189 4056 -
obs--96.27 %

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