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- PDB-3pz2: Crystal structure of RabGGTase(DELTA LRR; DELTA IG) in Complex wi... -

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Basic information

Entry
Database: PDB / ID: 3pz2
TitleCrystal structure of RabGGTase(DELTA LRR; DELTA IG) in Complex with BMS3 and lipid substrate GGPP
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-3PZ / GERANYLGERANYL DIPHOSPHATE / 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: 2.35 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 / Refinement description / 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)76,3436
Polymers75,2602
Non-polymers1,0844
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-23 kcal/mol
Surface area25140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.448, 84.582, 117.973
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 , 5 types, 187 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-3PZ / (3R)-3-benzyl-4-[(4-methoxyphenyl)sulfonyl]-1-[(1-methyl-1H-imidazol-5-yl)methyl]-2,3,4,5-tetrahydro-1H-1,4-benzodiazepine-7-carbonitrile


Mass: 527.637 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H29N5O3S
#6: Chemical ChemComp-GRG / GERANYLGERANYL DIPHOSPHATE


Mass: 450.443 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H36O7P2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.2 Å3/Da / Density % sol: 44.15 %
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: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 12, 2008
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→30 Å / Num. all: 28375 / Num. obs: 28201 / % possible obs: 99.4 % / Observed criterion σ(I): 5 / Redundancy: 4.9 % / Biso Wilson estimate: 42.4 Å2 / Rsym value: 0.063 / Net I/σ(I): 17.5
Reflection shellResolution: 2.35→2.45 Å / Redundancy: 5 % / Mean I/σ(I) obs: 7.1 / Num. unique all: 3230 / Rsym value: 0.377 / % possible all: 99

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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: 2.35→30 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.895 / SU B: 17.044 / SU ML: 0.186 / Cross valid method: THROUGHOUT / ESU R Free: 0.269 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25551 1403 5 %RANDOM
Rwork0.18761 ---
obs0.19095 26810 99.5 %-
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: 37.329 Å2
Baniso -1Baniso -2Baniso -3
1--1.18 Å20 Å20 Å2
2--1.47 Å20 Å2
3----0.3 Å2
Refinement stepCycle: LAST / Resolution: 2.35→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4920 0 69 183 5172
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0225121
X-RAY DIFFRACTIONr_bond_other_d00.023423
X-RAY DIFFRACTIONr_angle_refined_deg1.6221.9736954
X-RAY DIFFRACTIONr_angle_other_deg4.2623.0018310
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4165624
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.00424.163233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.37515861
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.321529
X-RAY DIFFRACTIONr_chiral_restr0.0960.2768
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025658
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021031
X-RAY DIFFRACTIONr_nbd_refined0.2430.21513
X-RAY DIFFRACTIONr_nbd_other0.2560.23754
X-RAY DIFFRACTIONr_nbtor_refined0.1880.22493
X-RAY DIFFRACTIONr_nbtor_other0.1140.22259
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.220.2279
X-RAY DIFFRACTIONr_metal_ion_refined0.0470.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2880.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2690.26
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1830.22
X-RAY DIFFRACTIONr_mcbond_it1.5671.53099
X-RAY DIFFRACTIONr_mcbond_other4.1441.51253
X-RAY DIFFRACTIONr_mcangle_it2.63824970
X-RAY DIFFRACTIONr_scbond_it3.52332022
X-RAY DIFFRACTIONr_scangle_it5.1644.51979
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 117 -
Rwork0.201 1896 -
obs--98.97 %
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)
10.00030.0005-0.00040.0009-0.00060.000400.0001-0.0002-0.0006-0.00050.0004-0.0001-0.00020.00050.01350.0003-0.0003-0.0024-0.0003-0.005814.54576.356416.7674
20.0003-0.00040.00020.0005-0.00020.00010.0002-0.0007-0.0005-0.0003-0.0003-0.00010-0.00020.00010.013200.0001-0.00240.0001-0.00593.389424.208517.8042
30000000000000000.00150.00050.00250.0014-0.00080.00120.57215.105223.5443
4000000000000000000000-8.407841.658529.3857
50.14950.06690.540.030.24181.95130.0323-0.0247-0.02490.01320.00470.0171-0.07240.085-0.0369-0.00010.00010-0.0004-0.0004-0.00065.102618.633127.1013
60.0026-0.0119-0.04280.05420.19450.69810.0020.0057-0.005-0.0021-0.0108-0.01410.00280.00960.0088-0.00070.0006-0.0003-0.0006-0.0003-0.00146.521216.956220.6547
70.0073-0.0005-0.00870.00230.00180.0109-0.0002-0.0027-0.0002-0.00030.00050.0002-0.0007-0.0008-0.00020.0120.0007-0.0006-0.00580.0004-0.00587.431117.433215.7709
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 DIFFRACTION5B333
6X-RAY DIFFRACTION6B334
7X-RAY DIFFRACTION7A331 - 394
8X-RAY DIFFRACTION7B335 - 453

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