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- PDB-4aii: Crystal structure of the rat REM2 GTPase - G domain bound to GDP -

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Basic information

Entry
Database: PDB / ID: 4aii
TitleCrystal structure of the rat REM2 GTPase - G domain bound to GDP
ComponentsGTP-BINDING PROTEIN REM 2
KeywordsGTP-BINDING PROTEIN / RGK PROTEINS
Function / homology
Function and homology information


calcium channel regulator activity / GTPase activity / GTP binding / signal transduction / membrane / plasma membrane
Similarity search - Function
Sigma-54 interaction domain, ATP-binding site 1 / Small GTPase, Ras-type / small GTPase Ras family profile. / Small GTPase / Ras family / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GTP-binding protein REM 2
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 Å
AuthorsReymond, P. / Coquard, A. / Chenon, M. / Zeghouf, M. / El Marjou, A. / Thompson, A. / Menetrey, J.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Structure of the Gdp-Bound G Domain of the Rgk Protein Rem2.
Authors: Reymond, P. / Coquard, A. / Chenon, M. / Zeghouf, M. / El Marjou, A. / Thompson, A. / Menetrey, J.
History
DepositionFeb 10, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2012Group: Other
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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_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_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_conn.ptnr2_label_seq_id / _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: GTP-BINDING PROTEIN REM 2
B: GTP-BINDING PROTEIN REM 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2426
Polymers40,3072
Non-polymers9354
Water21612
1
A: GTP-BINDING PROTEIN REM 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6213
Polymers20,1541
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GTP-BINDING PROTEIN REM 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6213
Polymers20,1541
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.916, 59.374, 57.297
Angle α, β, γ (deg.)90.00, 101.51, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1113A113 - 136
2113B113 - 136
1213A150 - 172
2213B150 - 172
1313A190 - 282
2313B190 - 282
1411A301 - 306
2411B301 - 306

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Components

#1: Protein GTP-BINDING PROTEIN REM 2 / RAD AND GEM-LIKE GTP-BINDING PROTEIN 2


Mass: 20153.689 Da / Num. of mol.: 2 / Fragment: G DOMAIN, RESIDUES 113-283
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9WTY2
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.58 % / Description: NONE
Crystal growDetails: 13.5 % PEG 4000, 10% ISOPROPANOL, 100 MM HEPES SODIUM SALT PH 7.4

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 6, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.66→41.65 Å / Num. obs: 9524 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 5.7
Reflection shellResolution: 2.66→2.8 Å / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CBQ

3cbq


Resolution: 2.66→41.65 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.832 / SU B: 14.91 / SU ML: 0.32 / Cross valid method: THROUGHOUT / ESU R: 3.941 / ESU R Free: 0.439 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 138-149 AND 171-182 ARE DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.32436 448 4.7 %RANDOM
Rwork0.24329 ---
obs0.24693 9160 98.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.842 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å20 Å20.64 Å2
2---5.06 Å20 Å2
3---6.09 Å2
Refinement stepCycle: LAST / Resolution: 2.66→41.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2174 0 58 12 2244
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0212298
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6331.9863115
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5835288
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.75821.15895
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.51515372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8421526
X-RAY DIFFRACTIONr_chiral_restr0.0930.2366
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021682
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.5751.51431
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.11622277
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9573867
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2754.5836
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
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A582tight positional0.030.05
2B582tight positional0.030.05
1A489loose positional0.045
2B489loose positional0.045
1A582tight thermal0.320.5
2B582tight thermal0.320.5
1A489loose thermal0.6510
2B489loose thermal0.6510
LS refinement shellResolution: 2.66→2.729 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 42 -
Rwork0.329 667 -
obs--98.34 %

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