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- PDB-4i1o: Crystal structure of the Legionella pneumophila GAP domain of Lep... -

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Basic information

Entry
Database: PDB / ID: 4i1o
TitleCrystal structure of the Legionella pneumophila GAP domain of LepB in complex with Rab1b bound to GDP and BeF3
Components
  • LepB
  • Ras-related protein Rab-1B
KeywordsPROTEIN TRANSPORT/HYDROLASE / GAP / RabGAP / hydrolase activator / Rab1b / lpg2490 / GTPase-activating proteins / hydrolysis / Rab1 hydrolase / GTP hydrolase / PROTEIN TRANSPORT-HYDROLASE complex
Function / homology
Function and homology information


positive regulation of glycoprotein metabolic process / phagophore assembly site membrane / RAB geranylgeranylation / regulation of autophagosome assembly / 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 / Golgi organization ...positive regulation of glycoprotein metabolic process / phagophore assembly site membrane / RAB geranylgeranylation / regulation of autophagosome assembly / 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 / Golgi organization / autophagosome assembly / endoplasmic reticulum to Golgi vesicle-mediated transport / transport vesicle / COPI-mediated anterograde transport / endomembrane system / endoplasmic reticulum-Golgi intermediate compartment membrane / small monomeric GTPase / intracellular protein transport / G protein activity / Golgi membrane / GTPase activity / endoplasmic reticulum membrane / GTP binding / perinuclear region of cytoplasm / Golgi apparatus / extracellular exosome / membrane / 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 ...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 Rab domain 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BERYLLIUM TRIFLUORIDE ION / GUANOSINE-5'-DIPHOSPHATE / DI(HYDROXYETHYL)ETHER / LepB / Ras-related protein Rab-1B
Similarity search - Component
Biological speciesHomo sapiens (human)
Legionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.701 Å
AuthorsGazdag, E.M. / Streller, A. / Vetter, I.R. / Goody, R.S. / Itzen, A.
CitationJournal: Embo Rep. / Year: 2013
Title: Mechanism of Rab1b deactivation by the Legionella pneumophila GAP LepB.
Authors: Mihai Gazdag, E. / Streller, A. / Haneburger, I. / Hilbi, H. / Vetter, I.R. / Goody, R.S. / Itzen, A.
History
DepositionNov 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)221,22726
Polymers218,4578
Non-polymers2,77118
Water2,630146
1
A: Ras-related protein Rab-1B
D: LepB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3607
Polymers54,6142
Non-polymers7465
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-21 kcal/mol
Surface area20550 Å2
MethodPISA
2
B: LepB
C: Ras-related protein Rab-1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4668
Polymers54,6142
Non-polymers8526
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-14 kcal/mol
Surface area20560 Å2
MethodPISA
3
E: Ras-related protein Rab-1B
F: LepB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1485
Polymers54,6142
Non-polymers5343
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-30 kcal/mol
Surface area20870 Å2
MethodPISA
4
G: Ras-related protein Rab-1B
H: LepB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2546
Polymers54,6142
Non-polymers6404
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-25 kcal/mol
Surface area20580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.410, 124.410, 147.470
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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Protein , 2 types, 8 molecules ACEGBDFH

#1: Protein
Ras-related protein Rab-1B


Mass: 20482.234 Da / Num. of mol.: 4 / Fragment: UNP residues 3-174
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB1B / Plasmid: pMAL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9H0U4
#2: Protein
LepB


Mass: 34131.914 Da / Num. of mol.: 4 / Fragment: GAP domain (UNP residues 317-618) / Mutation: K457A, E458A, K460A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: lepB, lpg2490 / Plasmid: pOPINM / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5ZSM7

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Non-polymers , 5 types, 164 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#5: Chemical
ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: BeF3
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 3.02 Å3/Da / Density % sol: 59.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 0.1 M sodium cacodylate, pH 6.4, 0.2 M magnesium chloride, 17% PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 9, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.7→49.157 Å / Num. obs: 70034 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 56.958 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 19.47
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.7-2.80.7173.671100
2.8-2.90.5524.821100
2.9-30.3916.61100
3-3.30.2529.681100
3.3-3.50.14315.441100
3.5-40.09423.21100
4-50.05833.981100
5-60.05834.961100
6-80.0538.61100
8-100.03852.531100
10-120.03453.681100
12-140.03655.5199.7
14-160.03654.311100
16-180.03754.931100
18-200.03752.961100
20-49.1570.04158.061100

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
XDSdata scaling
PHASERMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3NKV AND 4I1M

3nkv

4i1m


Resolution: 2.701→49.157 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.27 / σ(F): 1.99 / Phase error: 28.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2486 3499 5 %
Rwork0.2174 --
obs0.2191 69987 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.3913 Å2
Refinement stepCycle: LAST / Resolution: 2.701→49.157 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13990 0 174 146 14310
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01414451
X-RAY DIFFRACTIONf_angle_d1.05719641
X-RAY DIFFRACTIONf_dihedral_angle_d16.9845038
X-RAY DIFFRACTIONf_chiral_restr0.072269
X-RAY DIFFRACTIONf_plane_restr0.0042468
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.701-2.73770.37081380.29992620X-RAY DIFFRACTION100
2.7377-2.77680.38011420.31342709X-RAY DIFFRACTION100
2.7768-2.81830.2971390.30742630X-RAY DIFFRACTION100
2.8183-2.86230.33121410.3062675X-RAY DIFFRACTION100
2.8623-2.90920.3181400.28582674X-RAY DIFFRACTION100
2.9092-2.95940.30621410.29232667X-RAY DIFFRACTION100
2.9594-3.01320.28611400.282667X-RAY DIFFRACTION100
3.0132-3.07110.28381400.27732658X-RAY DIFFRACTION100
3.0711-3.13380.28991400.2832656X-RAY DIFFRACTION100
3.1338-3.20190.30391400.27172657X-RAY DIFFRACTION100
3.2019-3.27640.29861410.26752675X-RAY DIFFRACTION100
3.2764-3.35830.3141390.2552634X-RAY DIFFRACTION100
3.3583-3.44910.27281410.24322688X-RAY DIFFRACTION100
3.4491-3.55060.25531390.23182642X-RAY DIFFRACTION100
3.5506-3.66510.26391390.22172631X-RAY DIFFRACTION100
3.6651-3.79610.24381410.22942695X-RAY DIFFRACTION100
3.7961-3.9480.26141390.20152641X-RAY DIFFRACTION100
3.948-4.12760.19681400.18162663X-RAY DIFFRACTION100
4.1276-4.34510.20631400.17332657X-RAY DIFFRACTION100
4.3451-4.61710.20431410.17212684X-RAY DIFFRACTION100
4.6171-4.97330.19521400.17982670X-RAY DIFFRACTION100
4.9733-5.47320.22461400.19072647X-RAY DIFFRACTION100
5.4732-6.26380.2521390.20092651X-RAY DIFFRACTION100
6.2638-7.88650.24891400.20392659X-RAY DIFFRACTION100
7.8865-49.16480.1951390.17152638X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1-0.0004-0.01780.0221-0.0256-0.02560.0147-0.0380.0245-0.0087-0.0590.12980.0053-0.04840.0124-0-0.15460.155-0.52790.24070.3984-0.454627.5121-38.4942-10.4225
20.022-0.02650.01670.1176-0.0120.08970.03310.0932-0.10990.0820.3586-0.0361-0.06450.0464-0-0.2074-0.1877-0.00220.3167-0.2050.169284.3306-49.258-11.1367
30.00640.01430.0215-0.02550.02250.0138-0.0306-0.0153-0.03930.02910.1304-0.079-0.0367-0.0009-0-0.1139-0.1407-0.49560.2442-0.3569-0.303596.8047-38.514711.9472
40.02880.04060.02870.14220.01960.10180.029-0.141-0.0207-0.10550.36240.0056-0.1193-0.1079-0-0.10090.211-0.05820.28880.21720.176439.8371-49.247312.6773
50.00290.0202-0.0276-0.0317-0.02540.0099-0.0094-0.0088-0.00480.02760.14260.0670.05490.0041-0-0.2277-0.19450.58270.18860.4259-0.416627.5536-105.103311.9351
60.026-0.0172-0.02090.0529-0.03570.04310.0980.08010.16210.11360.5347-0.15810.07970.0209-0-0.1867-0.23180.0560.25810.2890.095940.088-94.267-11.1924
70.003-0.0208-0.018-0.02160.02020.0166-0.01690.0155-0.0097-0.04430.1325-0.04460.0756-0.01550-0.10290.18740.47750.2174-0.4365-0.339896.8944-105.1754-10.4108
80.02520.0425-0.02380.08970.01620.05610.1003-0.0730.1207-0.12160.37810.03660.10390.07090-0.28790.24780.05740.2592-0.22750.138884.5757-94.409312.6757
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 4:180)
2X-RAY DIFFRACTION2(chain B and resid 328:618)
3X-RAY DIFFRACTION3(chain C and resid 4:180)
4X-RAY DIFFRACTION4(chain D and resid 327:618)
5X-RAY DIFFRACTION5(chain E and resid 4:180)
6X-RAY DIFFRACTION6(chain F and resid 327:618)
7X-RAY DIFFRACTION7(chain G and resid 4:180)
8X-RAY DIFFRACTION8(chain H and resid 327:618)

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