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- PDB-4gtt: Engineered RabGGTase in complex with BMS analogue 12 -

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Basic information

Entry
Database: PDB / ID: 4gtt
TitleEngineered RabGGTase in complex with BMS analogue 12
Components(Geranylgeranyl transferase type-2 subunit ...) x 2
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / protein prenylation / inhibitor / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


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 / isoprenoid binding / Rab geranylgeranyltransferase activity / protein geranylgeranylation / endoplasmic reticulum to Golgi vesicle-mediated transport / 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 alpha-alpha toroid domain / 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-7TQ / 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: 2.05 Å
AuthorsGuo, Z. / Stigter, E.A. / Bon, R.S. / Waldmann, H. / Blankenfeldt, W. / Goody, R.S.
CitationJournal: J.Med.Chem. / Year: 2012
Title: Development of Selective, Potent RabGGTase Inhibitors
Authors: Stigter, E.A. / Guo, Z. / Bon, R.S. / Wu, Y.W. / Choidas, A. / Wolf, A. / Menninger, S. / Waldmann, H. / Blankenfeldt, W. / Goody, R.S.
History
DepositionAug 29, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.2Nov 8, 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_ref_seq_dif / 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_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_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_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_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_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_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)75,8475
Polymers75,0642
Non-polymers7823
Water6,233346
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-26 kcal/mol
Surface area26270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.592, 91.618, 114.305
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Geranylgeranyl transferase type-2 subunit ... , 2 types, 2 molecules AB

#1: Protein Geranylgeranyl transferase type-2 subunit alpha / 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 / Fragment: residues 1-237 and 353-441 linked with AGSG
Source method: isolated from a genetically manipulated source
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 / 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: Rabggtb, Ggtb / Plasmid: pET27b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CODON-PLUS RIL (DE3)
References: UniProt: Q08603, protein geranylgeranyltransferase type II

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Non-polymers , 4 types, 349 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-7TQ / 4-({(3R)-7-cyano-4-[(4-methoxyphenyl)sulfonyl]-1-[(1-methyl-1H-imidazol-5-yl)methyl]-2,3,4,5-tetrahydro-1H-1,4-benzodiazepin-3-yl}methyl)phenyl benzylcarbamate


Mass: 676.784 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H36N6O5S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / 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: 2.32 Å3/Da / Density % sol: 47.04 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: RabGGTase in 20mM Hepes pH7.2, 100mM NaCl and 2mM DTT was mixed with 15% PEG3350, 0.2M Ca Acetate, 0.1M Hepes pH7.2. The obtained crystals was soaked with 20% PEG3350, 0.2M Ca Acetate, 5% ...Details: RabGGTase in 20mM Hepes pH7.2, 100mM NaCl and 2mM DTT was mixed with 15% PEG3350, 0.2M Ca Acetate, 0.1M Hepes pH7.2. The obtained crystals was soaked with 20% PEG3350, 0.2M Ca Acetate, 5% Glycerol in the presence of 1mM inhibitor for 12 hour., VAPOR DIFFUSION, HANGING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→20 Å / Num. all: 44639 / Num. obs: 44335 / % possible obs: 99.3 % / Redundancy: 4.1 % / Biso Wilson estimate: 41.4 Å2 / Rsym value: 0.043 / Net I/σ(I): 19.5
Reflection shellResolution: 2.05→2.15 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 4.1 / Rsym value: 0.361 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
PHASESphasing
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DSS

3dss


Resolution: 2.05→19.99 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.931 / SU B: 10.171 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23323 2227 5 %RANDOM
Rwork0.17621 ---
obs0.17903 42081 99.41 %-
all-44639 --
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: 37.353 Å2
Baniso -1Baniso -2Baniso -3
1-1.61 Å20 Å20 Å2
2---0.14 Å20 Å2
3----1.48 Å2
Refinement stepCycle: LAST / Resolution: 2.05→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4995 0 51 346 5392
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0225226
X-RAY DIFFRACTIONr_bond_other_d00.023493
X-RAY DIFFRACTIONr_angle_refined_deg1.2051.977118
X-RAY DIFFRACTIONr_angle_other_deg4.1663.0028517
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7785653
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.77224.11236
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.52615861
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9541529
X-RAY DIFFRACTIONr_chiral_restr0.0730.2785
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025837
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021080
X-RAY DIFFRACTIONr_nbd_refined0.230.21567
X-RAY DIFFRACTIONr_nbd_other0.2370.23655
X-RAY DIFFRACTIONr_nbtor_refined0.1820.22590
X-RAY DIFFRACTIONr_nbtor_other0.1070.22237
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2130.2436
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.350.22
X-RAY DIFFRACTIONr_metal_ion_refined0.1270.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2220.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1150.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1130.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2151.53195
X-RAY DIFFRACTIONr_mcbond_other3.0031.51288
X-RAY DIFFRACTIONr_mcangle_it2.1225124
X-RAY DIFFRACTIONr_scbond_it2.66932031
X-RAY DIFFRACTIONr_scangle_it4.1974.51983
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 168 -
Rwork0.202 3067 -
obs--99.94 %
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)
10.00190.00110.00480.00450.00520.0132-0.0001-0.0003-0.00070-0.0007-0.0006-0.0002-0.0010.00080.00870.000100.01160.00020.010713.85516.87316.3031
20.0009-0.00030.0030.01550.00760.01480.001-0.001-0.0001-0.0001-0.0034-0.0001-0.0005-0.00410.00240.00830.00020.00030.0127-0.00090.01063.136626.23118.0211
3000000000000000-0.00010.00010.0001-0.00010-0.0001-0.21216.948223.4043
42.95192.0487-3.18161.426-2.24673.7837-0.0148-0.0308-0.0253-0.2090.0016-0.21490.11090.06650.0131-0.0004-0.0003-0.0005-0.0001-0.0001-0.00074.609121.823225.3261
5000000000000000000000-8.390144.294528.9426
60.00050.00080.00060.00140.00110.00080.0002-0.00010.0001-0.0001-0.0003-0.00030.0002-0.00020.00010.00900.00020.0119-0.00010.01058.408315.525314.7804
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 330
2X-RAY DIFFRACTION2B5 - 331
3X-RAY DIFFRACTION3B401
4X-RAY DIFFRACTION4B403
5X-RAY DIFFRACTION5B402
6X-RAY DIFFRACTION6A401 - 575
7X-RAY DIFFRACTION6B501 - 671

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