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- PDB-3q85: Crystal Structure of Rem2 G-domain -GTP Analog Complex -

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Basic information

Entry
Database: PDB / ID: 3q85
TitleCrystal Structure of Rem2 G-domain -GTP Analog Complex
ComponentsGTP-binding protein REM 2
KeywordsSIGNALING PROTEIN / G-domain / G-protein / Cav2 beta
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
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / THIOCYANATE ION / GTP-binding protein REM 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.757 Å
AuthorsNavon-Perry, L. / Hirsch, J.A.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: RGK Family G-Domain:GTP Analog Complex Structures and Nucleotide-Binding Properties.
Authors: Sasson, Y. / Navon-Perry, L. / Huppert, D. / Hirsch, J.A.
History
DepositionJan 6, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2011Group: Database references
Revision 1.2Sep 13, 2023Group: 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 / 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 / _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_asym_id / _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_asym_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_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

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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)39,1029
Polymers37,8352
Non-polymers1,2677
Water7,855436
1
A: GTP-binding protein REM 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5224
Polymers18,9171
Non-polymers6053
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)19,5805
Polymers18,9171
Non-polymers6634
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.525, 59.080, 56.144
Angle α, β, γ (deg.)90.00, 101.26, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein GTP-binding protein REM 2 / Rad and Gem-like GTP-binding protein 2


Mass: 18917.383 Da / Num. of mol.: 2 / Fragment: G-domain, rsidues 114-282
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rem2 / Plasmid: pET21d / Production host: Escherichia coli (E. coli) / References: UniProt: Q8VEL9
#2: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CNS
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 436 / 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: 2.26 Å3/Da / Density % sol: 45.53 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20%(w/v) PEG3350, 0.5M potassium thiocyanate and 7% glycerol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 20, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.757→50 Å / Num. all: 31389 / Num. obs: 31389 / % possible obs: 93.2 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.088 / Rsym value: 0.01247 / Net I/σ(I): 10.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
1.757-1.792.40.4891.39711.03758.1
1.79-1.822.50.4291.411611.11369.3
1.82-1.862.60.4781.513091.16379.1
1.86-1.92.70.391.914141.10284.3
1.9-1.942.70.392.115441.27991.6
1.94-1.982.80.3132.815871.2294.8
1.98-2.032.80.2673.316181.19497.2
2.03-2.092.90.2713.716651.49798.9
2.09-2.152.90.2324.516521.34198.8
2.15-2.222.90.1855.616551.36499.3
2.22-2.32.90.1616.516691.28199.2
2.3-2.392.90.1357.816911.33599.7
2.39-2.52.90.1288.616431.4199.7
2.5-2.632.90.1149.517111.3799.8
2.63-2.792.90.08812.316631.35699.8
2.79-3.012.90.06914.416881.18699.9
3.01-3.312.90.0519.516871.11499.5
3.31-3.792.90.03825.616771.06299.2
3.79-4.782.90.03623.816881.13899
4.78-502.90.04120.516961.12897.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(AutoMR)model building
PHENIX(phenix.refine: dev_412)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX(AutoMR)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CBQ

3cbq


Resolution: 1.757→40.281 Å / SU ML: 0.22 / σ(F): 0.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2353 1438 5.1 %RANDOM
Rwork0.2077 ---
obs0.2092 28191 83.65 %-
all-28204 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.773 Å2 / ksol: 0.388 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.3846 Å2-0 Å2-0.4436 Å2
2---0.4291 Å2-0 Å2
3---0.8138 Å2
Refinement stepCycle: LAST / Resolution: 1.757→40.281 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2332 0 75 436 2843
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052466
X-RAY DIFFRACTIONf_angle_d1.0193339
X-RAY DIFFRACTIONf_dihedral_angle_d13.866906
X-RAY DIFFRACTIONf_chiral_restr0.052385
X-RAY DIFFRACTIONf_plane_restr0.003416
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7573-1.82010.3618630.34261496X-RAY DIFFRACTION46
1.8201-1.89290.34351050.31392022X-RAY DIFFRACTION64
1.8929-1.97910.33071230.26182428X-RAY DIFFRACTION76
1.9791-2.08340.28271410.23352656X-RAY DIFFRACTION84
2.0834-2.2140.25781590.21892813X-RAY DIFFRACTION89
2.214-2.38490.22171600.20172912X-RAY DIFFRACTION91
2.3849-2.62480.27541810.19822987X-RAY DIFFRACTION94
2.6248-3.00460.20251570.19633096X-RAY DIFFRACTION97
3.0046-3.7850.19781740.17533168X-RAY DIFFRACTION98
3.785-40.29170.21781750.20093175X-RAY DIFFRACTION97

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