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- PDB-4iru: Crystal Structure of lepB GAP core in a transition state mimetic ... -

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Basic information

Entry
Database: PDB / ID: 4iru
TitleCrystal Structure of lepB GAP core in a transition state mimetic complex with Rab1A and ALF3
Components
  • LepB
  • Ras-related protein Rab-1A
KeywordsHYDROLASE/HYDROLASE / Arginine finger / Glutamate finger / P-loop motif / Nucleotide binding / Intrinsic GTPase activity / GTP hydrolysis / GTP hydrolysis activator / GTPase activating protein (GAP) / Protein transport / HYDROLASE-HYDROLASE complex
Function / homology
Function and homology information


positive regulation of glycoprotein metabolic process / growth hormone secretion / melanosome transport / COPII-coated vesicle cargo loading / vesicle transport along microtubule / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / Golgi Cisternae Pericentriolar Stack Reorganization / COPII-mediated vesicle transport / COPI-dependent Golgi-to-ER retrograde traffic ...positive regulation of glycoprotein metabolic process / growth hormone secretion / melanosome transport / COPII-coated vesicle cargo loading / vesicle transport along microtubule / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / Golgi Cisternae Pericentriolar Stack Reorganization / COPII-mediated vesicle transport / COPI-dependent Golgi-to-ER retrograde traffic / transport vesicle membrane / Golgi organization / virion assembly / autophagosome assembly / endoplasmic reticulum to Golgi vesicle-mediated transport / COPI-mediated anterograde transport / endomembrane system / G protein activity / small monomeric GTPase / substrate adhesion-dependent cell spreading / vesicle-mediated transport / intracellular protein transport / positive regulation of interleukin-8 production / autophagy / melanosome / endocytosis / cell migration / early endosome / cadherin binding / GTPase activity / Golgi membrane / defense response to bacterium / GTP binding / Golgi apparatus / endoplasmic reticulum / extracellular exosome / integral component of membrane / cytosol
Similarity search - Function
Four Helix Bundle (Hemerythrin (Met), subunit A) - #1700 / LepB GAP domain, C-terminal subdomain / LepB GAP domain N-terminal subdomain / LepB GAP domain C-terminal subdomain / LepB N-terminal domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #830 / LepB, N-terminal / LepB GAP domain, N-terminal subdomain / small GTPase Rab1 family profile. / Rho (Ras homology) subfamily of Ras-like small GTPases ...Four Helix Bundle (Hemerythrin (Met), subunit A) - #1700 / LepB GAP domain, C-terminal subdomain / LepB GAP domain N-terminal subdomain / LepB GAP domain C-terminal subdomain / LepB N-terminal domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #830 / LepB, N-terminal / LepB GAP domain, N-terminal subdomain / small GTPase Rab1 family profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras family / Small GTPase / Four Helix Bundle (Hemerythrin (Met), subunit A) / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Small GTP-binding protein domain / Alpha Horseshoe / 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 / ACETATE ION / ALUMINUM FLUORIDE / : / GUANOSINE-5'-DIPHOSPHATE / LepB
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.2 Å
AuthorsMishra, A.K. / Delcampo, C.M. / Collins, R.E. / Roy, C.R. / Lambright, D.G.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: The Legionella pneumophila GTPase Activating Protein LepB Accelerates Rab1 Deactivation by a Non-canonical Hydrolytic Mechanism.
Authors: Mishra, A.K. / Del Campo, C.M. / Collins, R.E. / Roy, C.R. / Lambright, D.G.
History
DepositionJan 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Sep 4, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LepB
B: Ras-related protein Rab-1A
C: LepB
D: Ras-related protein Rab-1A
E: LepB
F: Ras-related protein Rab-1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,60941
Polymers165,2746
Non-polymers3,33435
Water61334
1
A: LepB
B: Ras-related protein Rab-1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,71921
Polymers55,0912
Non-polymers1,62819
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7680 Å2
ΔGint-28 kcal/mol
Surface area20600 Å2
MethodPISA
2
C: LepB
D: Ras-related protein Rab-1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,24715
Polymers55,0912
Non-polymers1,15513
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5860 Å2
ΔGint-30 kcal/mol
Surface area21040 Å2
MethodPISA
3
E: LepB
F: Ras-related protein Rab-1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6435
Polymers55,0912
Non-polymers5513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-28 kcal/mol
Surface area21950 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)139.404, 139.404, 384.519
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

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Protein , 2 types, 6 molecules ACEBDF

#1: Protein LepB


Mass: 33916.312 Da / Num. of mol.: 3 / Fragment: LepB GAP domain, catalytic core
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: lepB, lpg2490 / Plasmid: pET28b (modified) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIPL / References: UniProt: Q5ZSM7, small monomeric GTPase
#2: Protein Ras-related protein Rab-1A / YPT1-related protein


Mass: 21175.166 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB1, RAB1A / Plasmid: pET15b (modified) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIPL / References: UniProt: P62820, small monomeric GTPase

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Non-polymers , 7 types, 69 molecules

#3: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-MG / MAGNESIUM ION


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


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#8: Chemical ChemComp-AF3 / ALUMINUM FLUORIDE / Aluminium fluoride


Mass: 83.977 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: AlF3
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.83 Å3/Da / Density % sol: 56.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 12% PEG4000, 0.1M Hepes, 0.2M potassium acetate, 0.002M aluminium chloride, 0.02M sodium fluoride, 0.01M 2-mercaptoethanol, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791, 0.9639
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 6, 2011 / Details: Mirrors
RadiationMonochromator: Double crystal monochromator with horizontal focusing
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.96391
ReflectionResolution: 3.2→50 Å / Num. obs: 30171 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Rsym value: 0.54 / Net I/σ(I): 3.8
Reflection shellResolution: 3.2→3.283 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 3.8 / Rsym value: 0.54 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
AutoSolin Phenixphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 3.2→43.01 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.852 / SU B: 25.04 / SU ML: 0.433 / Cross valid method: THROUGHOUT / ESU R Free: 0.577
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.28812 1602 5 %RANDOM
Rwork0.22954 ---
obs0.23247 30171 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 72.798 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å20 Å2
2--0.56 Å20 Å2
3----1.12 Å2
Refinement stepCycle: LAST / Resolution: 3.2→43.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11175 0 201 34 11410
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0211574
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4451.98215632
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.55251390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.42325.087519
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.608152030
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3851545
X-RAY DIFFRACTIONr_chiral_restr0.0930.21759
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218548
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 105 -
Rwork0.28 2227 -
obs--99.96 %

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