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- PDB-4wnr: Structure of methanosarcina barkeri Roco2 RocCORdC bound to GDP -

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Basic information

Entry
Database: PDB / ID: 4wnr
TitleStructure of methanosarcina barkeri Roco2 RocCORdC bound to GDP
ComponentsLeucine-rich-repeat protein
KeywordsSIGNALING PROTEIN / Roco proteins / GAD / small G-protein / COR / Parkinson's disease
Function / homology
Function and homology information


C-terminal of Roc (COR) domain / C-terminal of Roc, COR, 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 / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily ...C-terminal of Roc (COR) domain / C-terminal of Roc, COR, 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 / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Leucine-rich-repeat protein
Similarity search - Component
Biological speciesMethanosarcina barkeri (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsTerheyden, S.
Funding support United States, 1items
OrganizationGrant numberCountry
Michael J. Fox Foundation United States
CitationJournal: Biochem.J. / Year: 2015
Title: Revisiting the Roco G-protein cycle.
Authors: Terheyden, S. / Ho, F.Y. / Gilsbach, B.K. / Wittinghofer, A. / Kortholt, A.
History
DepositionOct 14, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: 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
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Leucine-rich-repeat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2926
Polymers40,5411
Non-polymers7525
Water34219
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-34 kcal/mol
Surface area16000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.360, 109.360, 223.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-802-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Leucine-rich-repeat protein


Mass: 40540.586 Da / Num. of mol.: 1 / Fragment: UNP residues 287-629
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina barkeri (archaea) / Strain: Fusaro / DSM 804 / Gene: Mbar_A2306 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q46A62

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Non-polymers , 5 types, 24 molecules

#2: 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
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 4.75 Å3/Da / Density % sol: 74.1 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: Tris, Sodiumsulfate, Lithiumsulfate, PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.06997 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.06997 Å / Relative weight: 1
ReflectionResolution: 2.9→49 Å / Num. all: 18169 / Num. obs: 18092 / % possible obs: 99.6 % / Redundancy: 8 % / Rsym value: 0.073 / Net I/σ(I): 21.84
Reflection shellResolution: 2.9→3.08 Å / Redundancy: 8.1 % / Mean I/σ(I) obs: 2.84 / Rsym value: 0.795 / % possible all: 98.6

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Processing

Software
NameVersionClassificationNB
REFMAC5.7.0029refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DPU

3dpu


Resolution: 2.9→48.06 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.919 / SU B: 13.548 / SU ML: 0.249 / Cross valid method: THROUGHOUT / ESU R: 0.455 / ESU R Free: 0.313 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26867 910 5 %RANDOM
Rwork0.24029 ---
obs0.24169 17272 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 83.25 Å2
Baniso -1Baniso -2Baniso -3
1--0.61 Å2-0.61 Å20 Å2
2---0.61 Å20 Å2
3---1.99 Å2
Refinement stepCycle: 1 / Resolution: 2.9→48.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2621 0 45 19 2685
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0192720
X-RAY DIFFRACTIONr_bond_other_d0.0050.022597
X-RAY DIFFRACTIONr_angle_refined_deg0.7691.993664
X-RAY DIFFRACTIONr_angle_other_deg0.6583.0035999
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4275322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.08324.8125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.51315512
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.2351511
X-RAY DIFFRACTIONr_chiral_restr0.0460.2397
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022981
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02606
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.462 65 -
Rwork0.369 1234 -
obs--99.46 %

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