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- PDB-3hxb: Engineered RabGGTase in complex with a peptidomimetic inhibitor (... -

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Basic information

Entry
Database: PDB / ID: 3hxb
TitleEngineered RabGGTase in complex with a peptidomimetic inhibitor (compound 6)
Components
  • Geranylgeranyl transferase type-2 subunit alpha
  • Geranylgeranyl transferase type-2 subunit beta
KeywordsTRANSFERASE / protein prenylation inhibition / Metal-binding / Prenyltransferase / Zinc
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
Rab geranylgeranyltransferase, alpha subunit, insert-domain / Rab geranylgeranyltransferase, alpha subunit, insert-domain superfamily / Rab geranylgeranyl transferase alpha-subunit, insert domain / Geranylgeranyl transferase type-2 subunit beta / Protein prenylyltransferase / Prenyltransferase subunit beta / Protein prenyltransferase, alpha subunit / Protein prenyltransferase alpha subunit repeat / Protein prenyltransferases alpha subunit repeat profile. / PFTB repeat ...Rab geranylgeranyltransferase, alpha subunit, insert-domain / Rab geranylgeranyltransferase, alpha subunit, insert-domain superfamily / Rab geranylgeranyl transferase alpha-subunit, insert domain / Geranylgeranyl transferase type-2 subunit beta / Protein prenylyltransferase / Prenyltransferase subunit beta / Protein prenyltransferase, alpha subunit / Protein prenyltransferase alpha subunit repeat / Protein prenyltransferases alpha subunit repeat profile. / PFTB repeat / Prenyltransferase and squalene oxidase repeat / Glycosyltransferase - #20 / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Glycosyltransferase / Alpha/alpha barrel / Leucine-rich repeat domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Chem-BD5 / Geranylgeranyl transferase type-2 subunit alpha / Geranylgeranyl transferase type-2 subunit beta
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsGuo, Z. / Alexandrov, K. / Waldmann, H. / Goody, R.S. / Blankenfeldt, W.
CitationJournal: J.Med.Chem. / Year: 2009
Title: Design, synthesis, and characterization of Peptide-based rab geranylgeranyl transferase inhibitors
Authors: Tan, K.T. / Guiu-Rozas, E. / Bon, R.S. / Guo, Z. / Delon, C. / Wetzel, S. / Arndt, S. / Alexandrov, K. / Waldmann, H. / Goody, R.S. / Wu, Y.W. / Blankenfeldt, W.
History
DepositionJun 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Sep 6, 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 / 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 / _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

Downloads & links

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Assembly

Deposited unit
A: Geranylgeranyl transferase type-2 subunit alpha
B: Geranylgeranyl transferase type-2 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0254
Polymers75,3342
Non-polymers6912
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-55 kcal/mol
Surface area26420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.490, 90.610, 115.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Geranylgeranyl transferase type-2 subunit alpha / 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) / Gene: Rabggta, Ggta / 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 Geranylgeranyl transferase type-2 subunit beta / 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) / Gene: Rabggtb, Ggtb / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon-Plus RIL (DE3)
References: UniProt: Q08603, protein geranylgeranyltransferase type II
#3: Chemical ChemComp-BD5 / N-[(benzyloxy)carbonyl]-D-tyrosyl-L-phenylalanyl-L-tyrosine


Mass: 625.668 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H35N3O8
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.3 Å3/Da / Density % sol: 46.6 %
Crystal growTemperature: 284 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 14% (w/v) PEG3350, 0.2 M Ca(OAc)2, 0.1 M HEPES, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 284K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9816 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 22, 2006
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9816 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. all: 33732 / Num. obs: 32922 / % possible obs: 97.6 % / Observed criterion σ(I): 4.9 / Redundancy: 4.9 % / Biso Wilson estimate: 43.7 Å2 / Rsym value: 0.052 / Net I/σ(I): 18.03
Reflection shellResolution: 2.25→2.35 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 4.86 / Num. unique all: 4004 / Rsym value: 0.327 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.2.0005refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3DSS

3dss


Resolution: 2.25→29.4 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.896 / SU B: 18.714 / SU ML: 0.206 / Cross valid method: THROUGHOUT / ESU R Free: 0.259 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; TLS-REFINEMENT WAS USED
RfactorNum. reflection% reflectionSelection details
Rfree0.27824 1634 5 %RANDOM
Rwork0.20667 ---
obs0.21016 31280 97.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 46.788 Å2
Baniso -1Baniso -2Baniso -3
1-2.33 Å20 Å20 Å2
2--0.47 Å20 Å2
3----2.8 Å2
Refinement stepCycle: LAST / Resolution: 2.25→29.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4918 0 47 125 5090
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0225085
X-RAY DIFFRACTIONr_bond_other_d00.024572
X-RAY DIFFRACTIONr_angle_refined_deg1.6421.9676910
X-RAY DIFFRACTIONr_angle_other_deg3.8113.00110539
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.635627
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.91523.937221
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.57715818
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0821528
X-RAY DIFFRACTIONr_chiral_restr0.1040.2771
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025661
X-RAY DIFFRACTIONr_gen_planes_other0.0090.021035
X-RAY DIFFRACTIONr_nbd_refined0.2220.21227
X-RAY DIFFRACTIONr_nbd_other0.2310.24308
X-RAY DIFFRACTIONr_nbtor_refined0.1860.22483
X-RAY DIFFRACTIONr_nbtor_other0.1110.22388
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2010.2168
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0220.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2820.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2350.27
X-RAY DIFFRACTIONr_mcbond_it1.7791.53147
X-RAY DIFFRACTIONr_mcbond_other2.1811.51276
X-RAY DIFFRACTIONr_mcangle_it2.97925020
X-RAY DIFFRACTIONr_scbond_it3.34331938
X-RAY DIFFRACTIONr_scangle_it4.9394.51890
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 109 -
Rwork0.262 2304 -
obs--99.18 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
10.20490.08980.37670.27370.23260.71210.0152-0.0033-0.05220.0208-0.0039-0.01520.0262-0.0059-0.0113-0.01560.01090.01280.00690.01550.0113.77256.60515.8574
20.22420.0040.0620.24820.09030.2515-0.0107-0.00670.01630-0.0196-0.0131-0.0094-0.05120.0303-0.0060.01140.01110.0039-0.00550.00612.886926.188117.8993
3000000000000000000000-0.3716.543523.7632
4000000000000000000000000
5000000000000000000000000
60.12060.02240.03110.00540.0040.0105-0.00790.0189-0.00150.00020.0038-0.0020.0020.00360.00410.022-0.0006-0.00010.0126-0.00190.03210.415515.037811.7938
722.074415.7635-2.161111.3019-1.49950.2541-0.33151.4799-0.5431.5168-0.15971.1123-0.05321.00070.4912-0.0013-0.0035-0.00140.00120.002-0.00056.551820.919423.0923
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 330
2X-RAY DIFFRACTION2B3 - 331
3X-RAY DIFFRACTION3B1 - 333
4X-RAY DIFFRACTION4Y1
5X-RAY DIFFRACTION5Z1
6X-RAY DIFFRACTION6A - B1 - 400
7X-RAY DIFFRACTION7B1 - 332

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