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- PDB-4jvs: Crystal structure of LepB GAP domain from Legionella drancourtii ... -

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Basic information

Entry
Database: PDB / ID: 4jvs
TitleCrystal structure of LepB GAP domain from Legionella drancourtii in complex with Rab1-GDP and AlF3
Components
  • Putative uncharacterized protein
  • Ras-related protein Rab-1A
KeywordsHYDROLASE ACTIVATOR/PROTEIN TRANSPORT / New GAP fold / Bind and hydrolyze guanosine triphosphate / Rab1 Binding / HYDROLASE ACTIVATOR-PROTEIN TRANSPORT 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 / virion assembly / transport vesicle membrane / Golgi organization / autophagosome assembly / endoplasmic reticulum to Golgi vesicle-mediated transport / endomembrane system / COPI-mediated anterograde transport / vesicle-mediated transport / substrate adhesion-dependent cell spreading / small monomeric GTPase / G protein activity / positive regulation of interleukin-8 production / intracellular protein transport / autophagy / endocytosis / melanosome / cell migration / membrane => GO:0016020 / early endosome / defense response to bacterium / cadherin binding / Golgi membrane / GTPase activity / GTP binding / Golgi apparatus / endoplasmic reticulum / extracellular exosome / cytosol
Similarity search - Function
Four Helix Bundle (Hemerythrin (Met), subunit A) - #1700 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #830 / LepB GAP domain, C-terminal subdomain / LepB, N-terminal / LepB GAP domain, N-terminal subdomain / LepB GAP domain N-terminal subdomain / LepB GAP domain C-terminal subdomain / LepB N-terminal domain / ARF-like small GTPases; ARF, ADP-ribosylation factor / small GTPase Rab1 family profile. ...Four Helix Bundle (Hemerythrin (Met), subunit A) - #1700 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #830 / LepB GAP domain, C-terminal subdomain / LepB, N-terminal / LepB GAP domain, N-terminal subdomain / LepB GAP domain N-terminal subdomain / LepB GAP domain C-terminal subdomain / LepB N-terminal domain / ARF-like small GTPases; ARF, ADP-ribosylation factor / small GTPase Rab1 family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Four Helix Bundle (Hemerythrin (Met), subunit A) / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / 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
ACETIC ACID / ALUMINUM FLUORIDE / GUANOSINE-5'-DIPHOSPHATE / Uncharacterized protein / Ras-related protein Rab-1A
Similarity search - Component
Biological speciesLegionella drancourtii (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.783 Å
AuthorsYu, Q. / Yao, Q. / Wang, D.-C. / Shao, F.
CitationJournal: Cell Res. / Year: 2013
Title: Structural analyses of Legionella LepB reveal a new GAP fold that catalytically mimics eukaryotic RasGAP
Authors: Yu, Q. / Hu, L. / Yao, Q. / Zhu, Y. / Dong, N. / Wang, D.-C. / Shao, F.
History
DepositionMar 26, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _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: Putative uncharacterized protein
B: Ras-related protein Rab-1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7236
Polymers56,1122
Non-polymers6124
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-30 kcal/mol
Surface area20750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.561, 95.561, 197.724
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Putative uncharacterized protein / GTPase activating protein


Mass: 35628.348 Da / Num. of mol.: 1 / Fragment: GAP domain, UNP residues 316-620
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella drancourtii (bacteria) / Strain: LLAP12 / Gene: LDG_7216 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G9EPL4
#2: Protein Ras-related protein Rab-1A / Ras superfamily of monomeric G protein / YPT1-related protein


Mass: 20483.225 Da / Num. of mol.: 1 / Fragment: UNP residues 1-177
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB1A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62820

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Non-polymers , 5 types, 8 molecules

#3: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#4: 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
#5: Chemical ChemComp-AF3 / ALUMINUM FLUORIDE / Aluminium fluoride


Mass: 83.977 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF3
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.32 Å3/Da / Density % sol: 47.03 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 8.5
Details: 0.2M ammonium acetate, 0.1M Tris, 25%(w/v) polyethylene glycol 3350, pH 8.5, EVAPORATION, temperature 298.0K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.78→20 Å / Num. obs: 14058 / % possible obs: 100 % / Biso Wilson estimate: 40.05 Å2

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASESphasing
PHENIX1.8_1069refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.783→19.96 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7934 / SU ML: 0.35 / σ(F): 1.37 / Phase error: 25.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2645 702 5.02 %
Rwork0.2236 13274 -
obs0.2256 13976 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 121.15 Å2 / Biso mean: 46.3017 Å2 / Biso min: 20 Å2
Refinement stepCycle: LAST / Resolution: 2.783→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3614 0 37 4 3655
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0193722
X-RAY DIFFRACTIONf_angle_d1.5035040
X-RAY DIFFRACTIONf_chiral_restr0.097556
X-RAY DIFFRACTIONf_plane_restr0.011648
X-RAY DIFFRACTIONf_dihedral_angle_d19.3731374
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7833-2.99750.37921490.29242538268798
2.9975-3.29790.29711280.267226082736100
3.2979-3.77240.27231480.227726152763100
3.7724-4.74220.2211460.187626592805100
4.7422-19.9610.23651310.209428542985100

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