- PDB-3hxc: Engineered RabGGTase in complex with a peptidomimetic inhibitor (... -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: PDB / ID: 3hxc
Title
Engineered RabGGTase in complex with a peptidomimetic inhibitor (compound 8)
Components
(Geranylgeranyl transferase type-2 subunit ...) x 2
Keywords
TRANSFERASE / protein prenylation inhibition
Function / homology
Function and homology information
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 geranylgeranyltransferase subunit alpha / ...Geranylgeranyl transferase type II subunit alpha / Rab geranylgeranyltransferase subunit alpha / Rab geranyl-geranyltransferase subunit alpha / Rab GG transferase alpha / Rab GGTase alpha
Mass: 38441.598 Da / Num. of mol.: 1 / Fragment: RabGGTase ALPHA-subunit / Mutation: DELTA LRR; DELTA IG Source method: isolated from a genetically manipulated source Details: coexpression of engineered alpha-subunit from pGATEV and beta-subunit from pET3 0a Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pGATEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon-Plus RIL (DE3) References: UniProt: Q08602, protein geranylgeranyltransferase type II
#2: Protein
Geranylgeranyltransferasetype-2subunitbeta / Geranylgeranyl transferase type II subunit beta / GGTase-II-beta / Type II protein geranyl- ...Geranylgeranyl transferase type II subunit beta / GGTase-II-beta / Type II protein geranyl-geranyltransferase subunit beta / Rab geranylgeranyltransferase subunit beta / Rab geranyl-geranyltransferase subunit beta / Rab GG transferase beta / Rab GGTase beta
Mass: 36892.160 Da / Num. of mol.: 1 / Fragment: RABGGTase BETA-subunit Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon-Plus RIL (DE3) References: UniProt: Q08603, protein geranylgeranyltransferase type II
Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 4, 2009
Radiation
Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9787 Å / Relative weight: 1
Reflection
Resolution: 1.95→30 Å / Num. all: 51454 / Num. obs: 51225 / % possible obs: 99.6 % / Observed criterion σ(I): 4.47 / Redundancy: 4.8 % / Biso Wilson estimate: 35.4 Å2 / Rsym value: 0.051 / Net I/σ(I): 18.79
Reflection shell
Resolution: 1.95→2.05 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 4.47 / Num. unique all: 7037 / Rsym value: 0.373 / % possible all: 100
-
Processing
Software
Name
Version
Classification
PHASER
phasing
REFMAC
5.2.0019
refinement
XDS
datareduction
XSCALE
datascaling
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→29.4 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.936 / SU B: 7.448 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; TLS-REFINEMENT WAS USED
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.21819
2578
5 %
RANDOM
Rwork
0.16936
-
-
-
obs
0.17175
48641
99.58 %
-
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: 32.582 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.2 Å2
0 Å2
0 Å2
2-
-
0.34 Å2
0 Å2
3-
-
-
-0.54 Å2
Refinement step
Cycle: LAST / Resolution: 1.95→29.4 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
4952
0
50
374
5376
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.009
0.022
5241
X-RAY DIFFRACTION
r_bond_other_d
0
0.02
3502
X-RAY DIFFRACTION
r_angle_refined_deg
1.123
1.964
7140
X-RAY DIFFRACTION
r_angle_other_deg
4.194
3.002
8504
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.121
5
655
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
35.12
24.06
234
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
14.274
15
860
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
15.775
15
28
X-RAY DIFFRACTION
r_chiral_restr
0.067
0.2
787
X-RAY DIFFRACTION
r_gen_planes_refined
0.004
0.02
5856
X-RAY DIFFRACTION
r_gen_planes_other
0.005
0.02
1074
X-RAY DIFFRACTION
r_nbd_refined
0.213
0.2
1425
X-RAY DIFFRACTION
r_nbd_other
0.236
0.2
3504
X-RAY DIFFRACTION
r_nbtor_refined
0.18
0.2
2600
X-RAY DIFFRACTION
r_nbtor_other
0.112
0.2
2173
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.19
0.2
399
X-RAY DIFFRACTION
r_metal_ion_refined
0.064
0.2
3
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.167
0.2
13
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.255
0.2
35
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.163
0.2
20
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
0.049
0.2
3
X-RAY DIFFRACTION
r_mcbond_it
1.056
1.5
3207
X-RAY DIFFRACTION
r_mcbond_other
2.304
1.5
1292
X-RAY DIFFRACTION
r_mcangle_it
1.843
2
5149
X-RAY DIFFRACTION
r_scbond_it
2.182
3
2034
X-RAY DIFFRACTION
r_scangle_it
3.236
4.5
1980
LS refinement shell
Resolution: 1.95→2 Å / Total num. of bins used: 20
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi