- PDB-3kkq: Crystal structure of M-Ras P40D in complex with GDP -
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Basic information
Entry
Database: PDB / ID: 3kkq
Title
Crystal structure of M-Ras P40D in complex with GDP
Components
Ras-related protein M-Ras
Keywords
SIGNALING PROTEIN / GTP-binding / GTPase
Function / homology
Function and homology information
RAF activation / GTP-dependent protein binding / small monomeric GTPase / G protein activity / cellular response to leukemia inhibitory factor / GDP binding / Ras protein signal transduction / GTPase activity / GTP binding / plasma membrane Similarity search - Function
Small GTPase, Ras-type / small GTPase Ras family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / 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 ...Small GTPase, Ras-type / small GTPase Ras family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology
Resolution: 1.2→29.51 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.953 / SU B: 0.466 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.038 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.19222
3159
5.1 %
RANDOM
Rwork
0.17576
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-
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all
0.17658
59019
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obs
0.17658
59019
98.18 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 10.329 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0 Å2
0 Å2
0 Å2
2-
-
0 Å2
0 Å2
3-
-
-
0 Å2
Refinement step
Cycle: LAST / Resolution: 1.2→29.51 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1387
0
29
243
1659
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.006
0.022
1445
X-RAY DIFFRACTION
r_angle_refined_deg
1.161
1.982
1961
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.425
5
169
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
36.544
24.444
72
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
11.436
15
256
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
16.952
15
9
X-RAY DIFFRACTION
r_chiral_restr
0.077
0.2
218
X-RAY DIFFRACTION
r_gen_planes_refined
0.004
0.02
1084
X-RAY DIFFRACTION
r_nbd_refined
0.192
0.2
678
X-RAY DIFFRACTION
r_nbtor_refined
0.311
0.2
997
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.097
0.2
185
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.155
0.2
35
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.088
0.2
22
X-RAY DIFFRACTION
r_mcbond_it
0.61
1.5
868
X-RAY DIFFRACTION
r_mcangle_it
0.991
2
1383
X-RAY DIFFRACTION
r_scbond_it
1.457
3
653
X-RAY DIFFRACTION
r_scangle_it
2.137
4.5
578
LS refinement shell
Resolution: 1.2→1.231 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.199
254
-
Rwork
0.19
4202
-
obs
-
4202
96.93 %
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