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- PDB-6hlu: Crystal structure of the LRR-Roc-COR domain of the Chlorobium tep... -

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Basic information

Entry
Database: PDB / ID: 6hlu
TitleCrystal structure of the LRR-Roc-COR domain of the Chlorobium tepidum Roco protein
ComponentsRab family protein
KeywordsHYDROLASE / GTPase / LRRK2 / Roco proteins
Function / homology
Function and homology information


GTP binding / identical protein binding
Similarity search - Function
C-terminal of Roc (COR) domain / C-terminal of Roc, COR, domain / Ras of Complex, Roc, domain of DAPkinase / Leucine rich repeat, ribonuclease inhibitor type / Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / Roc domain profile. / Roc domain / Leucine Rich repeat / Leucine-rich repeats, bacterial type ...C-terminal of Roc (COR) domain / C-terminal of Roc, COR, domain / Ras of Complex, Roc, domain of DAPkinase / Leucine rich repeat, ribonuclease inhibitor type / Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / Roc domain profile. / Roc domain / Leucine Rich repeat / Leucine-rich repeats, bacterial type / 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
Similarity search - Domain/homology
Biological speciesChlorobaculum tepidum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.29 Å
AuthorsDeyaert, E. / Versees, W. / Singh, R.
Funding support Belgium, United States, 2items
OrganizationGrant numberCountry
Research Foundation - Flanders Belgium
Michael J. Fox Foundation United States
CitationJournal: Biochem. J. / Year: 2019
Title: Structure and nucleotide-induced conformational dynamics of theChlorobium tepidumRoco protein.
Authors: Deyaert, E. / Leemans, M. / Singh, R.K. / Gallardo, R. / Steyaert, J. / Kortholt, A. / Lauer, J. / Versees, W.
History
DepositionSep 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 26, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Jan 24, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)219,4772
Polymers219,4772
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-13 kcal/mol
Surface area70940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.586, 129.756, 179.465
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: 109738.711 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlorobaculum tepidum (bacteria) / Gene: CT1526 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8KC98

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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: 2.75 Å3/Da / Density % sol: 55.26 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.8 M Sodium Formate, 0.1 M Sodium Acetate pH 5.5, 10% PEG8000, 10% PEG 1000
PH range: 5.5-6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 3.29→47.8 Å / Num. obs: 34302 / % possible obs: 99 % / Redundancy: 4.5 % / Biso Wilson estimate: 86.144159769 Å2 / CC1/2: 0.995 / Rrim(I) all: 0.158 / Net I/σ(I): 9.3
Reflection shellResolution: 3.29→3.4 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3210 / CC1/2: 0.539 / Rrim(I) all: 1.103 / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3dpu and 5il7

3dpu

5il7


Resolution: 3.29→44.848 Å / SU ML: 0.55 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.36
RfactorNum. reflection% reflectionSelection details
Rfree0.2806 1685 4.91 %RANDOM
Rwork0.2296 ---
obs0.2321 34297 99.17 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.29→44.848 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13681 0 0 0 13681
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00213915
X-RAY DIFFRACTIONf_angle_d0.54818974
X-RAY DIFFRACTIONf_dihedral_angle_d2.5838460
X-RAY DIFFRACTIONf_chiral_restr0.0432300
X-RAY DIFFRACTIONf_plane_restr0.0042430
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.29-3.38670.43651290.39562499X-RAY DIFFRACTION93
3.3867-3.4960.40021430.3552692X-RAY DIFFRACTION100
3.496-3.62090.37771200.30772709X-RAY DIFFRACTION100
3.6209-3.76580.36121460.27582690X-RAY DIFFRACTION100
3.7658-3.93710.32711500.25572716X-RAY DIFFRACTION100
3.9371-4.14450.27431380.23852713X-RAY DIFFRACTION100
4.1445-4.4040.26781550.20932673X-RAY DIFFRACTION99
4.404-4.74370.26251360.1962730X-RAY DIFFRACTION99
4.7437-5.22040.24261450.19612724X-RAY DIFFRACTION99
5.2204-5.97430.25831370.22712774X-RAY DIFFRACTION100
5.9743-7.52120.26681440.22252773X-RAY DIFFRACTION100
7.5212-44.85170.22071420.17942919X-RAY DIFFRACTION100

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