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- PDB-5il7: Leucine rich repeat domain of the Chlorobium tepidum Roco protein -

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Basic information

Entry
Database: PDB / ID: 5il7
TitleLeucine rich repeat domain of the Chlorobium tepidum Roco protein
ComponentsRab family protein
KeywordsSIGNALING PROTEIN / Leucine rich repeat domain
Function / homology
Function and homology information


non-specific serine/threonine protein kinase / protein serine/threonine kinase activity / GTP binding / ATP binding / identical protein binding
Similarity search - Function
: / : / C-terminal of Roc, COR-B domain / C-terminal of Roc (COR) domain / C-terminal of Roc, COR-A domain / Ras of Complex, Roc, domain of DAPkinase / Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / Roc domain profile. / Roc domain ...: / : / C-terminal of Roc, COR-B domain / C-terminal of Roc (COR) domain / C-terminal of Roc, COR-A domain / Ras of Complex, Roc, domain of DAPkinase / Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / Roc domain profile. / Roc domain / Leucine rich repeat, ribonuclease inhibitor type / Leucine Rich repeat / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Leucine-rich repeats, bacterial type / Alpha-Beta Horseshoe / Leucine-rich repeat, SDS22-like subfamily / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Rab subfamily of small GTPases / Leucine-rich repeat domain superfamily / Small GTP-binding protein domain / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Alpha Beta
Similarity search - Domain/homology
non-specific serine/threonine protein kinase
Similarity search - Component
Biological speciesChlorobium tepidum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGotthardt, K. / Wittinghofer, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Structural model of the dimeric Parkinson's protein LRRK2 reveals a compact architecture involving distant interdomain contacts.
Authors: Guaitoli, G. / Raimondi, F. / Gilsbach, B.K. / Gomez-Llorente, Y. / Deyaert, E. / Renzi, F. / Li, X. / Schaffner, A. / Jagtap, P.K. / Boldt, K. / von Zweydorf, F. / Gotthardt, K. / Lorimer, ...Authors: Guaitoli, G. / Raimondi, F. / Gilsbach, B.K. / Gomez-Llorente, Y. / Deyaert, E. / Renzi, F. / Li, X. / Schaffner, A. / Jagtap, P.K. / Boldt, K. / von Zweydorf, F. / Gotthardt, K. / Lorimer, D.D. / Yue, Z. / Burgin, A. / Janjic, N. / Sattler, M. / Versees, W. / Ueffing, M. / Ubarretxena-Belandia, I. / Kortholt, A. / Gloeckner, C.J.
History
DepositionMar 4, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2016Group: Database references
Revision 1.2Jul 13, 2016Group: Database references
Revision 1.3Aug 10, 2016Group: Database references
Revision 1.4Jan 25, 2017Group: Database references
Revision 1.5May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rab family protein
B: Rab family protein


Theoretical massNumber of molelcules
Total (without water)97,4082
Polymers97,4082
Non-polymers00
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-2 kcal/mol
Surface area33970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.223, 98.941, 155.397
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 Rab family protein


Mass: 48703.914 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlorobium tepidum (strain ATCC 49652 / DSM 12025 / NBRC 103806 / TLS) (bacteria)
Gene: CT1526 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: Q8KC98
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.1 Å3/Da / Density % sol: 41.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Na Acetate, 2.2 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 17, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→47.14 Å / Num. obs: 37250 / % possible obs: 99.8 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.1 / Rsym value: 0.12 / Net I/σ(I): 13.77
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 4.42 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 106v

106v


Resolution: 2.3→47.14 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.899 / SU B: 8.363 / SU ML: 0.2 / Cross valid method: THROUGHOUT / ESU R: 0.468 / ESU R Free: 0.269 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26082 1863 5 %RANDOM
Rwork0.21417 ---
obs0.21649 35387 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 29.868 Å2
Baniso -1Baniso -2Baniso -3
1-1.62 Å20 Å2-0 Å2
2---2.2 Å20 Å2
3---0.58 Å2
Refinement stepCycle: LAST / Resolution: 2.3→47.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6720 0 0 99 6819
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.026876
X-RAY DIFFRACTIONr_bond_other_d0.0010.026706
X-RAY DIFFRACTIONr_angle_refined_deg1.1242.0099378
X-RAY DIFFRACTIONr_angle_other_deg0.771315588
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.395904
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.28627.115260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.484151286
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4651519
X-RAY DIFFRACTIONr_chiral_restr0.0610.21171
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217685
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021302
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_it0.9022.9693544
X-RAY DIFFRACTIONr_mcbond_other0.9012.9673543
X-RAY DIFFRACTIONr_mcangle_it1.5744.4464433
X-RAY DIFFRACTIONr_mcangle_other1.5744.4484434
X-RAY DIFFRACTIONr_scbond_it0.9333.0973332
X-RAY DIFFRACTIONr_scbond_other0.9333.0993333
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.6284.5894932
X-RAY DIFFRACTIONr_long_range_B_refined2.9322.8147157
X-RAY DIFFRACTIONr_long_range_B_other2.92522.8127150
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 134 -
Rwork0.255 2551 -
obs--99.89 %

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