isoprenoid binding / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / protein geranylgeranyltransferase type II / RAB geranylgeranylation / Rab-protein geranylgeranyltransferase complex / Rab geranylgeranyltransferase activity / protein geranylgeranylation / small GTPase binding / zinc ion binding / cytoplasm Similarity search - Function
Geranylgeranyltransferasetype-2subunitalpha / Geranylgeranyl transferase type II subunit alpha / Rab geranyl-geranyltransferase subunit alpha / ...Geranylgeranyl transferase type II subunit alpha / Rab geranyl-geranyltransferase subunit alpha / Rab GG transferase alpha / Rab GGTase alpha / Rab geranylgeranyltransferase subunit alpha
Mass: 38303.453 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: UNP residues 1-237 and 353-441 from Geranylgeranyl transferase type-2 subunit alpha (Q08602, PGTA_RAT) connected by a linker Ala-Gly-Ser-Gly. Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ggta, Rabggta / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL References: UniProt: Q08602, protein geranylgeranyltransferase type II
#2: Protein
Geranylgeranyltransferasetype-2subunitbeta / Geranylgeranyl transferase type II subunit beta / GGTase-II-beta / Rab geranyl-geranyltransferase ...Geranylgeranyl transferase type II subunit beta / GGTase-II-beta / Rab geranyl-geranyltransferase subunit beta / Rab GG transferase beta / Rab GGTase beta / Rab geranylgeranyltransferase subunit beta / Type II protein geranyl-geranyltransferase subunit beta
Mass: 36760.965 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ggtb, Rabggtb / Production host: Escherichia coli (E. coli) / Strain (production host): bl21(DE3)RIL References: UniProt: Q08603, protein geranylgeranyltransferase type II
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→29.4 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.913 / SU B: 14.376 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.25148
1795
5 %
RANDOM
Rwork
0.18552
-
-
-
obs
0.18875
34152
99.75 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 42.542 Å2
Baniso -1
Baniso -2
Baniso -3
1-
1.15 Å2
0 Å2
0 Å2
2-
-
0.47 Å2
0 Å2
3-
-
-
-1.61 Å2
Refinement step
Cycle: LAST / Resolution: 2.2→29.4 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
5067
0
27
319
5413
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.014
0.022
5263
X-RAY DIFFRACTION
r_bond_other_d
0
0.02
3517
X-RAY DIFFRACTION
r_angle_refined_deg
1.409
1.966
7164
X-RAY DIFFRACTION
r_angle_other_deg
4.499
3.001
8570
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.426
5
659
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
36.205
24.274
241
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
16.329
15
875
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
15.964
15
29
X-RAY DIFFRACTION
r_chiral_restr
0.079
0.2
790
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.02
5883
X-RAY DIFFRACTION
r_gen_planes_other
0.007
0.02
1064
X-RAY DIFFRACTION
r_nbd_refined
0.218
0.2
1368
X-RAY DIFFRACTION
r_nbd_other
0.231
0.2
3671
X-RAY DIFFRACTION
r_nbtor_refined
0.184
0.2
2613
X-RAY DIFFRACTION
r_nbtor_other
0.123
0.2
2353
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.208
0.2
309
X-RAY DIFFRACTION
r_metal_ion_refined
0.073
0.2
1
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.149
0.2
10
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.248
0.2
29
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.17
0.2
18
X-RAY DIFFRACTION
r_mcbond_it
1.152
1.5
3236
X-RAY DIFFRACTION
r_mcbond_other
3.807
1.5
1311
X-RAY DIFFRACTION
r_mcangle_it
2.06
2
5187
X-RAY DIFFRACTION
r_scbond_it
2.006
3
2027
X-RAY DIFFRACTION
r_scangle_it
3.102
4.5
1967
LS refinement shell
Resolution: 2.2→2.257 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.327
135
-
Rwork
0.249
2481
-
obs
-
-
99.85 %
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°2)
L12 (°2)
L13 (°2)
L22 (°2)
L23 (°2)
L33 (°2)
S11 (Å °)
S12 (Å °)
S13 (Å °)
S21 (Å °)
S22 (Å °)
S23 (Å °)
S31 (Å °)
S32 (Å °)
S33 (Å °)
T11 (Å2)
T12 (Å2)
T13 (Å2)
T22 (Å2)
T23 (Å2)
T33 (Å2)
Origin x (Å)
Origin y (Å)
Origin z (Å)
1
0.0002
0.0002
0.0006
0.0002
0.0005
0.0015
0.0002
-0.0001
-0.0001
0.0001
0
-0.0003
0.0003
-0.0001
-0.0002
-0.0021
-0.0001
0
-0.0009
0.0001
0.0071
13.5963
6.8433
16.2554
2
0.0007
0.0005
0.0006
0.004
0.001
0.0005
-0.0001
0.0001
0.0005
0.0003
-0.0001
0.0003
0.0003
-0.0001
0.0002
-0.0023
0
0.0001
-0.0007
0
0.0069
2.8693
25.754
18.171
3
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
-0.735
16.4096
23.6857
4
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
-8.3957
43.8606
29.3183
5
0
0
-0.0001
0
0
0.0014
0
-0.0001
-0.0003
-0.0002
-0.0002
0.0001
0.0001
0
0.0002
-0.0022
0
0
-0.0008
-0.0002
0.0068
10.535
14.0102
12.1063
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
1 - 330
2
X-RAY DIFFRACTION
1
A
401
3
X-RAY DIFFRACTION
2
B
5 - 331
4
X-RAY DIFFRACTION
3
B
401
5
X-RAY DIFFRACTION
4
B
402
6
X-RAY DIFFRACTION
5
A
501 - 659
7
X-RAY DIFFRACTION
5
B
501 - 660
+
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