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- PDB-1tno: Rat Protein Geranylgeranyltransferase Type-I Complexed with a GGP... -

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Basic information

Entry
Database: PDB / ID: 1tno
TitleRat Protein Geranylgeranyltransferase Type-I Complexed with a GGPP analog and a KKKSKTKCVIM Peptide Derived from K-Ras4B
Components
  • Geranylgeranyl transferase type I beta subunit
  • c-K-ras2 protein isoform b
  • geranylgeranyltransferase type I alpha subunit
KeywordsTRANSFERASE / GGTase-I / geranylgeranyltransferase type-I / geranylgeranyl transferase / prenyltransferase / CaaX / Ras / K-Ras / Lipid modification / prenylation / substrate selectivity
Function / homology
Function and homology information


Apoptotic cleavage of cellular proteins / Inactivation, recovery and regulation of the phototransduction cascade / RAS processing / protein geranylgeranyltransferase activity / peptide pheromone maturation / protein farnesylation / protein geranylgeranyltransferase type I / CAAX-protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase complex / positive regulation of tubulin deacetylation ...Apoptotic cleavage of cellular proteins / Inactivation, recovery and regulation of the phototransduction cascade / RAS processing / protein geranylgeranyltransferase activity / peptide pheromone maturation / protein farnesylation / protein geranylgeranyltransferase type I / CAAX-protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase complex / positive regulation of tubulin deacetylation / protein farnesyltransferase / protein farnesyltransferase activity / protein farnesyltransferase complex / Rab geranylgeranyltransferase activity / protein geranylgeranylation / positive regulation of skeletal muscle acetylcholine-gated channel clustering / : / microtubule associated complex / heterocyclic compound binding / enzyme-linked receptor protein signaling pathway / : / positive regulation of Rac protein signal transduction / alpha-tubulin binding / positive regulation of cell cycle / response to cytokine / : / receptor tyrosine kinase binding / microtubule binding / molecular adaptor activity / positive regulation of cell population proliferation / negative regulation of apoptotic process / zinc ion binding / cytoplasm
Similarity search - Function
Geranylgeranyl transferase type-1 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 ...Geranylgeranyl transferase type-1 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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Chem-MGM / Geranylgeranyl transferase type-1 subunit beta / Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsReid, T.S. / Terry, K.L. / Casey, P.J. / Beese, L.S.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Crystallographic analysis of CaaX prenyltransferases complexed with substrates defines rules of protein substrate selectivity.
Authors: Reid, T.S. / Terry, K.L. / Casey, P.J. / Beese, L.S.
History
DepositionJun 11, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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_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_asym_id / _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_asym_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_asym_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_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: geranylgeranyltransferase type I alpha subunit
B: Geranylgeranyl transferase type I beta subunit
C: geranylgeranyltransferase type I alpha subunit
D: Geranylgeranyl transferase type I beta subunit
E: geranylgeranyltransferase type I alpha subunit
F: Geranylgeranyl transferase type I beta subunit
G: geranylgeranyltransferase type I alpha subunit
H: Geranylgeranyl transferase type I beta subunit
I: geranylgeranyltransferase type I alpha subunit
J: Geranylgeranyl transferase type I beta subunit
K: geranylgeranyltransferase type I alpha subunit
L: Geranylgeranyl transferase type I beta subunit
M: c-K-ras2 protein isoform b
N: c-K-ras2 protein isoform b
O: c-K-ras2 protein isoform b
P: c-K-ras2 protein isoform b
Q: c-K-ras2 protein isoform b
R: c-K-ras2 protein isoform b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)530,82436
Polymers527,17818
Non-polymers3,64518
Water12,214678
1
A: geranylgeranyltransferase type I alpha subunit
B: Geranylgeranyl transferase type I beta subunit
M: c-K-ras2 protein isoform b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,5776
Polymers87,8633
Non-polymers7143
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8580 Å2
ΔGint-69 kcal/mol
Surface area25880 Å2
MethodPISA
2
C: geranylgeranyltransferase type I alpha subunit
D: Geranylgeranyl transferase type I beta subunit
N: c-K-ras2 protein isoform b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,4176
Polymers87,8633
Non-polymers5543
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8490 Å2
ΔGint-82 kcal/mol
Surface area26110 Å2
MethodPISA
3
E: geranylgeranyltransferase type I alpha subunit
F: Geranylgeranyl transferase type I beta subunit
O: c-K-ras2 protein isoform b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,6137
Polymers87,8633
Non-polymers7504
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8740 Å2
ΔGint-82 kcal/mol
Surface area26110 Å2
MethodPISA
4
G: geranylgeranyltransferase type I alpha subunit
H: Geranylgeranyl transferase type I beta subunit
P: c-K-ras2 protein isoform b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,4176
Polymers87,8633
Non-polymers5543
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8490 Å2
ΔGint-84 kcal/mol
Surface area25990 Å2
MethodPISA
5
I: geranylgeranyltransferase type I alpha subunit
J: Geranylgeranyl transferase type I beta subunit
Q: c-K-ras2 protein isoform b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,3825
Polymers87,8633
Non-polymers5192
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8360 Å2
ΔGint-74 kcal/mol
Surface area26170 Å2
MethodPISA
6
K: geranylgeranyltransferase type I alpha subunit
L: Geranylgeranyl transferase type I beta subunit
R: c-K-ras2 protein isoform b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,4176
Polymers87,8633
Non-polymers5543
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8540 Å2
ΔGint-84 kcal/mol
Surface area26520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)272.531, 268.484, 185.940
Angle α, β, γ (deg.)90.00, 131.48, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 12 molecules ACEGIKBDFHJL

#1: Protein
geranylgeranyltransferase type I alpha subunit / Type I protein geranyl-geranyltransferase alpha subunit / GGTase-I-alpha


Mass: 44098.145 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: FNTA / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q04631, protein geranylgeranyltransferase type I
#2: Protein
Geranylgeranyl transferase type I beta subunit / Type I protein geranyl-geranyltransferase beta subunit / GGTase-I-beta


Mass: 42466.176 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: PGGT1B / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P53610, protein geranylgeranyltransferase type I

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Protein/peptide , 1 types, 6 molecules MNOPQR

#3: Protein/peptide
c-K-ras2 protein isoform b


Mass: 1298.723 Da / Num. of mol.: 6 / Fragment: c-terminus / Source method: obtained synthetically
Details: THE SUBSTRATE PEPTIDE WAS CHEMICALLY SYNTHESIZED. The sequence of this peptide naturally exists in Homo sapiens (Human).

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Non-polymers , 5 types, 696 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Chemical
ChemComp-MGM / 2-[METHYL-(5-GERANYL-4-METHYL-PENT-3-ENYL)-AMINO]-ETHYL-DIPHOSPHATE / 3-AZAGERANYLGERANYL DIPHOSPHATE


Mass: 453.447 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C19H37NO7P2
#7: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 678 / 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: 5.6 Å3/Da / Density % sol: 77.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 1.3 M ammonium sulfate, 175 mM NaCitrate pH 6.5, 100 mM MES pH 6.3, 20 mM DTT, 1uM ZnCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.07172 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 7, 2002
Details: Elliptically bent mirror/sagittal focusing second monochromator crystal
RadiationMonochromator: Si (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07172 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 272486 / Num. obs: 251777 / % possible obs: 92.2 % / Observed criterion σ(F): -0.5 / Observed criterion σ(I): -0.5 / Redundancy: 2.5 % / Biso Wilson estimate: 60.7 Å2 / Rsym value: 0.065 / Net I/σ(I): 12.3
Reflection shellResolution: 2.7→2.8 Å / Mean I/σ(I) obs: 2.5 / Rsym value: 0.193 / % possible all: 79.2

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Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N4Q

1n4q


Resolution: 2.7→29.98 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 341774.47 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): -0.5 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.211 12637 5 %RANDOM
Rwork0.194 ---
all0.194 272961 --
obs0.194 251777 92.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.6173 Å2 / ksol: 0.364197 e/Å3
Displacement parametersBiso mean: 64.9 Å2
Baniso -1Baniso -2Baniso -3
1--8.55 Å20 Å2-6.22 Å2
2--13.95 Å20 Å2
3----5.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 2.7→29.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32406 0 208 678 33292
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.341.5
X-RAY DIFFRACTIONc_mcangle_it2.292
X-RAY DIFFRACTIONc_scbond_it2.132
X-RAY DIFFRACTIONc_scangle_it3.332.5
LS refinement shellResolution: 2.7→2.8 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.34 1087 5.1 %
Rwork0.313 20435 -
obs--79.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3ION.PARAMAGP.TOP
X-RAY DIFFRACTION4AGP.PARION.TOP
X-RAY DIFFRACTION5MES.PARMES.TOP

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