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- PDB-4i1m: Crystal structure of the Legionella pneumophila GAP domain of LepB -

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Basic information

Entry
Database: PDB / ID: 4i1m
TitleCrystal structure of the Legionella pneumophila GAP domain of LepB
ComponentsLepB
KeywordsHYDROLASE / RabGAP / hydrolase activator / Rab1b / lpg2490 / GTPase-activating proteins / hydrolysis / Rab1 hydrolase / GTP hydrolase
Function / homology
Function and homology information


microtubule organizing center / membrane
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 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat ...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 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / LepB
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.804 Å
AuthorsStreller, A. / Gazdag, E.M. / 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, 2017Group: Data collection / Category: pdbx_diffrn_reflns_shell / Item: _pdbx_diffrn_reflns_shell.percent_possible_obs
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: LepB
B: LepB
C: LepB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,5024
Polymers102,3963
Non-polymers1061
Water50428
1
A: LepB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2382
Polymers34,1321
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LepB


Theoretical massNumber of molelcules
Total (without water)34,1321
Polymers34,1321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: LepB


Theoretical massNumber of molelcules
Total (without water)34,1321
Polymers34,1321
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)152.700, 152.700, 129.500
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-801-

HOH

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Components

#1: Protein LepB


Mass: 34131.914 Da / Num. of mol.: 3 / 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
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 3.69 Å3/Da / Density % sol: 66.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Bicine, pH 7.5, 0.75 M lithium chloride, 6% PEG6000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSLS X10SA11
SYNCHROTRONSLS X10SA20.9793
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXELJul 11, 2011
DECTRIS PILATUS 6M2PIXELAug 11, 2011
Radiation
IDMonochromatorProtocolScattering typeWavelength-ID
1double crystal Si(111)SINGLE WAVELENGTHx-ray1
2double crystal Si(111)SINGLE WAVELENGTHx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97931
ReflectionNumber: 543871 / Rmerge(I) obs: 0.166 / D res high: 3.4 Å / Num. obs: 40231 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
15.2149.8344097.310.039
10.7515.2182310010.037
8.7810.75107410010.04
7.68.78125910010.051
6.87.6143310010.076
6.216.8158710010.101
5.756.21172010010.129
5.385.75185010010.171
5.075.38197710010.173
4.815.07205710010.173
4.584.81220310010.197
4.394.58229410010.224
4.224.39238810010.271
4.064.22245210010.332
3.934.06255610010.417
3.83.93268610010.529
3.693.8276110010.651
3.583.69280110010.868
3.493.58291910011.096
3.43.49295110011.401
ReflectionResolution: 2.8→49.831 Å / Num. all: 38042 / Num. obs: 38042 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13.29 % / Biso Wilson estimate: 66.273 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 24.36
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.8-2.870.7373.51363912773100
2.87-2.950.6154.27356392700100
2.95-3.040.4795.56367852624100
3.04-3.130.3647.3352562539100
3.13-3.230.3058.58340822482100
3.23-3.350.21811.79323942394100
3.35-3.470.16715.17297832318100
3.47-3.610.12819.31294642241100
3.61-3.780.10224.42291772136100
3.78-3.960.08129.96282392061100
3.96-4.170.06834.99265821970100
4.17-4.430.0639.42244961862100
4.43-4.730.05443.06224811761100
4.73-5.110.05244.73218211644100
5.11-5.60.05442.6320518151299.9
5.6-6.260.0543.89181171386100
6.26-7.230.04448.29149631237100
7.23-8.850.03660.53136741054100
8.85-12.520.03166.4210045849100
12.520.03166.89560149997.8

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 4.42 Å / D res low: 50 Å / FOM : 0.34 / Reflection: 10061
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se600.2150.1330.2471.496
2Se600.4450.2620.2521.36
3Se600.4470.2520.0441.834
4Se600.6230.3620.1241.536
5Se600.6940.2630.1251.228
6Se600.7510.1170.1941.158
7Se600.1170.1750.190.857
8Se600.4120.0240.0091.052
9Se600.2360.3560.1740.733
Phasing MAD shell
Resolution (Å)FOM Reflection
15.61-500.38546
9.95-15.610.41855
7.81-9.950.421071
6.64-7.810.381259
5.87-6.640.351390
5.32-5.870.331522
4.9-5.320.311668
4.56-4.90.281750

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
SOLVE2.13phasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.804→49.831 Å / Occupancy max: 1 / Occupancy min: 0.31 / FOM work R set: 0.8245 / SU ML: 0.33 / σ(F): 2.02 / σ(I): -3 / Phase error: 24.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1902 5 %RANDOM
Rwork0.1995 ---
obs0.2015 38034 99.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 183.01 Å2 / Biso mean: 76.5663 Å2 / Biso min: 23.97 Å2
Refinement stepCycle: LAST / Resolution: 2.804→49.831 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6483 0 7 28 6518
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036642
X-RAY DIFFRACTIONf_angle_d0.6769039
X-RAY DIFFRACTIONf_chiral_restr0.0511033
X-RAY DIFFRACTIONf_plane_restr0.0031167
X-RAY DIFFRACTIONf_dihedral_angle_d15.1722304
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.804-2.87460.30091300.24142500263098
2.8746-2.95230.26731330.239725292662100
2.9523-3.03920.28321360.239125502686100
3.0392-3.13730.28861340.231125402674100
3.1373-3.24940.27821350.244225532688100
3.2494-3.37940.28391330.224925452678100
3.3794-3.53320.22921340.211325512685100
3.5332-3.71940.2571350.206325772712100
3.7194-3.95240.22431350.190325632698100
3.9524-4.25740.2371360.18225772713100
4.2574-4.68550.21511360.174325982734100
4.6855-5.36290.23051390.18526132752100
5.3629-6.7540.25161380.221126482786100
6.754-49.83860.2051480.179427882936100
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)
12.0548-1.20010.42694.3217-1.30582.6021-0.0125-0.01020.0829-0.1630.0051-0.1320.162-0.08550.01690.2612-0.09230.03040.2511-0.02130.400230.414217.690855.907
24.18292.0202-1.44313.2809-0.84622.8267-0.0085-0.0171-0.0933-0.1478-0.0785-0.4372-0.09910.15480.02370.35970.0541-0.02640.25570.02870.329729.119-10.805267.6
36.4129-0.1799-1.71542.59920.7513.4106-0.10570.4225-1.1704-0.3967-0.0660.17280.599-0.4520.15810.6425-0.11920.02730.32890.0450.404134.404622.682526.6536
42.3273-0.0356-0.99571.2502-0.45993.43420.0253-0.1260.1776-0.00080.0037-0.1919-0.13150.8127-0.00670.4315-0.02910.06250.42080.0270.359453.34535.242832.9541
50.3880.54210.89373.4699-1.85723.5021-0.3438-0.0340.0370.25790.0941-0.0291-1.67190.54540.24231.6767-0.1678-0.09710.6241-0.19340.821348.9892-12.445826.2757
60.0503-0.3090.06241.4291.57230.61010.18220.02410.06310.00770.1179-0.2173-1.31730.9005-0.33081.6574-0.4049-0.04581.0475-0.12350.86355.4537-1.0864-1.7821
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 322:518)A322 - 518
2X-RAY DIFFRACTION2(chain A and resid 519:618)A519 - 618
3X-RAY DIFFRACTION3(chain B and resid 327:393)B327 - 393
4X-RAY DIFFRACTION4(chain B and resid 399:617)B399 - 617
5X-RAY DIFFRACTION5(chain C and resid 317:516)C317 - 516
6X-RAY DIFFRACTION6(chain C and resid 517:617)C517 - 617

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