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- PDB-3q7q: Crystal Structure of Rad G-domain Q148A-GTP Analog Complex -

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Basic information

Entry
Database: PDB / ID: 3q7q
TitleCrystal Structure of Rad G-domain Q148A-GTP Analog Complex
ComponentsGTP-binding protein RAD
KeywordsSIGNALING PROTEIN / G-domain / G-protein / Cav2 beta
Function / homology
Function and homology information


NGF-stimulated transcription / small GTPase-mediated signal transduction / calcium channel regulator activity / calmodulin binding / GTPase activity / GTP binding / plasma membrane / cytosol
Similarity search - Function
Ras-related small G protein, RGK family / small GTPase Ras family profile. / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold ...Ras-related small G protein, RGK family / small GTPase Ras family profile. / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / 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 / GTP-binding protein RAD
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSasson, Y. / Navon-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 5, 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_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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_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 RAD
B: GTP-binding protein RAD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5977
Polymers36,4632
Non-polymers1,1335
Water70339
1
A: GTP-binding protein RAD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8184
Polymers18,2321
Non-polymers5873
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GTP-binding protein RAD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7783
Polymers18,2321
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.370, 38.370, 154.111
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 94:111 )
211chain B and (resseq 94:111 )
112chain A and (resseq 163:184 )
212chain B and (resseq 163:184 )
113chain A and (resseq 197:250 )
213chain B and (resseq 197:250 )

NCS ensembles :
ID
1
2
3

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Components

#1: Protein GTP-binding protein RAD / RAD1 / Ras associated with diabetes


Mass: 18231.715 Da / Num. of mol.: 2 / Fragment: G-domain, residues 90-255 / Mutation: Q148A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RRAD, RAD / Plasmid: pET21d / Production host: Escherichia coli (E. coli) / References: UniProt: P55042
#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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 1.8 Å3/Da / Density % sol: 31.52 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.7
Details: 12% PEG 8000, 0.1M MES, 0.2M calcium acetate, pH 5.7, VAPOR DIFFUSION, SITTING DROP, temperature 292.0K

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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 21, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 11324 / Num. obs: 11324 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 20.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
2.3-2.383.30.4962.21071193.6
2.38-2.483.70.4452.911211100
2.48-2.593.80.343.911461100
2.59-2.733.80.2655.611491100
2.73-2.93.80.1758.811431100
2.9-3.123.80.12512.711111100
3.12-3.443.70.07519.31143199.8
3.44-3.933.60.05621.21157199.8
3.93-4.953.80.03932.11131199.6
4.95-504.40.02942.51152199.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(Auto.MR)model building
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX(Auto.MR)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q7P

3q7p


Resolution: 2.3→33.229 Å / σ(F): 0.13 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.201 1112 10.06 %RANDOM
Rwork0.166 ---
obs0.1696 11052 97.52 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.965 Å2 / ksol: 0.348 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.105 Å2-0 Å20 Å2
2---1.105 Å2-0 Å2
3---2.21 Å2
Refinement stepCycle: LAST / Resolution: 2.3→33.229 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2179 0 67 39 2285
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042283
X-RAY DIFFRACTIONf_angle_d0.973094
X-RAY DIFFRACTIONf_dihedral_angle_d20.567813
X-RAY DIFFRACTIONf_chiral_restr0.057353
X-RAY DIFFRACTIONf_plane_restr0.004386
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A120X-RAY DIFFRACTIONPOSITIONAL
12B120X-RAY DIFFRACTIONPOSITIONAL0.063
21A167X-RAY DIFFRACTIONPOSITIONAL
22B167X-RAY DIFFRACTIONPOSITIONAL0.02
31A415X-RAY DIFFRACTIONPOSITIONAL
32B415X-RAY DIFFRACTIONPOSITIONAL0.064
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / % reflection obs: 98 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.3-2.43940.33391600.264315411541
2.4394-2.62770.25521860.238816331633
2.6277-2.8920.27751900.205117031703
2.892-3.31020.2181760.186616901690
3.3102-4.16920.17781860.137917141714
4.1692-33.23290.1621950.137716781678

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