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- PDB-3pz3: Crystal structure of RabGGTase(DELTA LRR; DELTA IG) in Complex wi... -

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Basic information

Entry
Database: PDB / ID: 3pz3
TitleCrystal structure of RabGGTase(DELTA LRR; DELTA IG) in Complex with BMS-analogue 14
Components(Geranylgeranyl transferase type-2 subunit ...) x 2
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / protein prenylation / fusion protein / chimera protein / 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-PZ3 / 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 Å
AuthorsGuo, Z. / Bon, R.S. / Stigter, E.A. / Waldmann, H. / Alexandrov, K. / Blankenfeldt, W. / Goody, R.S.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2011
Title: Structure-Guided Development of Selective RabGGTase Inhibitors.
Authors: Bon, R.S. / Guo, Z. / Stigter, E.A. / Wetzel, S. / Menninger, S. / Wolf, A. / Choidas, A. / Alexandrov, K. / Blankenfeldt, W. / Goody, R.S. / Waldmann, H.
History
DepositionDec 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 15, 2014Group: Database references / Source and taxonomy
Revision 1.3Aug 9, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Sep 13, 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.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_conn.ptnr2_label_seq_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)76,1115
Polymers75,2602
Non-polymers8513
Water5,999333
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-28 kcal/mol
Surface area26210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.732, 91.332, 114.652
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: 38498.652 Da / Num. of mol.: 1 / Fragment: UNP residues 1-237 and 353-441
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 and pET30a / 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 / Fragment: UNP residues 10-339
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: Rabggtb, Ggtb / Plasmid: pGATEV and pET30a / 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, 336 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-PZ3 / 4-({(3R)-7-(5-formylfuran-2-yl)-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: 745.843 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H39N5O7S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / 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: 47.01 %
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: 0.977 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 31, 2009
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 48077 / Num. obs: 47598 / % possible obs: 99 % / Observed criterion σ(I): 5 / Redundancy: 3.7 % / Biso Wilson estimate: 37.3 Å2 / Rsym value: 0.041 / Net I/σ(I): 20.5
Reflection shellResolution: 2→2.1 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 4.8 / Num. unique all: 6416 / Rsym value: 0.354 / % possible all: 99.6

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Processing

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

3dss


Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.937 / SU B: 8.846 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22368 2389 5 %RANDOM
Rwork0.17849 ---
obs0.18072 45177 99.07 %-
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: 36.218 Å2
Baniso -1Baniso -2Baniso -3
1-1.15 Å20 Å20 Å2
2---0.28 Å20 Å2
3----0.87 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5006 0 56 333 5395
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225231
X-RAY DIFFRACTIONr_bond_other_d00.023521
X-RAY DIFFRACTIONr_angle_refined_deg1.1941.9727117
X-RAY DIFFRACTIONr_angle_other_deg4.1793.0018538
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0755646
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.91524.083240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.38615875
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7511531
X-RAY DIFFRACTIONr_chiral_restr0.0740.2781
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025822
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021061
X-RAY DIFFRACTIONr_nbd_refined0.2140.21339
X-RAY DIFFRACTIONr_nbd_other0.2310.23513
X-RAY DIFFRACTIONr_nbtor_refined0.1820.22573
X-RAY DIFFRACTIONr_nbtor_other0.1090.22266
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.2352
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.3640.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1650.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3060.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.221
X-RAY DIFFRACTIONr_mcbond_it1.2071.53174
X-RAY DIFFRACTIONr_mcbond_other3.0661.51280
X-RAY DIFFRACTIONr_mcangle_it2.07825097
X-RAY DIFFRACTIONr_scbond_it2.69732057
X-RAY DIFFRACTIONr_scangle_it4.2784.52011
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 181 -
Rwork0.212 3261 -
obs--99.54 %
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)
10.00060.00040.00140.00020.00090.0037-0.00010.00010.00010-0.00010.00030.00020.00030.00030.00280.000100.01230.0001-0.000713.98966.739515.8141
20.0018000000.0001-0.0003-0.00020.0001-0.0002-0.0001-0.0001-0.00040.00010.00290.000100.01220-0.00052.966425.988718.0633
30000000000000000.0003-0.00020.00010.0001-0.0001-0.0001-0.51316.866923.5589
4000000000000000000000-8.149843.871729.1968
50.0009-0.0002-0.001100.00020.00130.00030.00060.00050.0001-0.00060.00010.0002-0.00010.00020.0029-0.000100.0117-0.0002-0.00029.982115.896114.7718
60.23040.4163-0.34080.7525-0.61590.50420.0259-0.0111-0.00080.0359-0.0278-0.0342-0.0026-0.04470.0019-0.00050.00010.0001-0.0002-0.0001-0.00024.263821.940125.3108
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 330
2X-RAY DIFFRACTION2B5 - 331
3X-RAY DIFFRACTION3B1
4X-RAY DIFFRACTION4B332
5X-RAY DIFFRACTION5A331 - 478
6X-RAY DIFFRACTION5B334 - 518
7X-RAY DIFFRACTION6B333

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