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- PDB-2ftz: Crystal structure of Geranyltranstransferase (EC 2.5.1.10) (tm016... -

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Basic information

Entry
Database: PDB / ID: 2ftz
TitleCrystal structure of Geranyltranstransferase (EC 2.5.1.10) (tm0161) from THERMOTOGA MARITIMA at 1.90 A resolution
Componentsgeranyltranstransferase
KeywordsTRANSFERASE / tm0161 / Geranyltranstransferase (EC 2.5.1.10) / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


geranylgeranyl diphosphate biosynthetic process / farnesyltranstransferase activity / prenyltransferase activity
Similarity search - Function
Polyprenyl synthases signature 1. / Polyprenyl synthases signature 2. / Polyprenyl synthetase, conserved site / Polyprenyl synthetase / Polyprenyl synthetase / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Unknown ligand / : / Geranyltranstransferase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Geranyltranstransferase (EC 2.5.1.10) (tm0161) from THERMOTOGA MARITIMA at 1.90 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJan 25, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 999SEQUENCE THE PROTEIN WAS REDUCTIVELY METHYLATED PRIOR TO CRYSTALLIZATION.
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: geranyltranstransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,80113
Polymers33,1811
Non-polymers62112
Water3,081171
1
A: geranyltranstransferase
hetero molecules

A: geranyltranstransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,60326
Polymers66,3622
Non-polymers1,24124
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area9090 Å2
ΔGint8 kcal/mol
Surface area21810 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)138.594, 138.594, 46.466
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-292-

HOH

21A-351-

HOH

DetailsSIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein geranyltranstransferase /


Mass: 33180.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: tm0161 / Plasmid: MH4a / Production host: Escherichia coli (E. coli)
References: GenBank: 4980655, UniProt: Q9WY08*PLUS, (2E,6E)-farnesyl diphosphate synthase
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 2 / Source method: obtained synthetically
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 3.32 Å3/Da / Density % sol: 62.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 10.5
Details: 0.2M NaCl, 20.0% PEG-8000, 0.1M CAPS pH 10.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9801 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 10, 2005
RadiationMonochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.9→29.62 Å / Num. obs: 36302 / % possible obs: 100 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 7.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsRsym value% possible all
1.9-1.9510060.4751.626200.475100
1.95-21007.10.386225670.386
2-2.061007.20.2682.825110.268
2.06-2.121007.10.2123.624360.212
2.12-2.191007.10.174.523590.17
2.19-2.271007.10.1365.522820.136
2.27-2.361007.10.1156.422280.115
2.36-2.451007.10.0947.721360.094
2.45-2.561007.10.0937.420430.093
2.56-2.6910070.0818.519510.081
2.69-2.8310070.0671018710.067
2.83-310070.05811.117870.058
3-3.211006.90.05212.216720.052
3.21-3.471006.80.04912.315760.049
3.47-3.81006.70.04812.414620.048
3.8-4.251006.60.04911.313240.049
4.25-4.911006.20.0511.511820.05
4.91-6.0199.96.10.04213.310080.042
6.01-8.51006.80.02918.78100.029
8.5-29.6296.55.90.02225.94770.022

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
SCALAdata scaling
PDB_EXTRACT1.7data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1rtr

1rtr


Resolution: 1.9→29.62 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.853 / SU ML: 0.057 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: (1) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS (2) RESIDUES OF 211-221 WEREN'T VISIBLE IN THE ELECTRON DENSITY MAPS. (3) ADDITIONAL DENSITY FOUND IN THE ACTIVE SITE WAS MODELED AS 2 ...Details: (1) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS (2) RESIDUES OF 211-221 WEREN'T VISIBLE IN THE ELECTRON DENSITY MAPS. (3) ADDITIONAL DENSITY FOUND IN THE ACTIVE SITE WAS MODELED AS 2 UNKNOWN LIGANDS (UNL). IT WAS NOT POSSIBLE TO UNAMBIGUOUSLY IDENTIFY THE LIGAND WITH THE AVAILABLE DATA. SOME POSSIBILITIES CONSIDERED WERE MULTIPLE CONFORMATIONS OF FPP (FARNESYL DIPHOSPHATE) OR MIXED CONFORMATION WITH DST (DIMETHYLALLYL S-THIOLODIPHOSPHATE), IPR (ISOPENTYL PYROPGOSPHATE) AND FPP. (4) ALL LYSINES ARE METHYLATED EXCEPT LYSINE 2, WHICH IS PROTECTED.
RfactorNum. reflection% reflectionSelection details
Rfree0.203 1807 5 %RANDOM
Rwork0.169 ---
all0.17 ---
obs0.17 36252 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.418 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å20 Å20 Å2
2---0.77 Å20 Å2
3---1.54 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2118 0 53 171 2342
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222244
X-RAY DIFFRACTIONr_bond_other_d0.0020.021590
X-RAY DIFFRACTIONr_angle_refined_deg1.4322999
X-RAY DIFFRACTIONr_angle_other_deg0.91433866
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4715263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.51923.81105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.11915.128430
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1021516
X-RAY DIFFRACTIONr_chiral_restr0.0940.2343
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022389
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02458
X-RAY DIFFRACTIONr_nbd_refined0.2580.2575
X-RAY DIFFRACTIONr_nbd_other0.180.21624
X-RAY DIFFRACTIONr_nbtor_refined0.180.21122
X-RAY DIFFRACTIONr_nbtor_other0.0870.21107
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.2146
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4210.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3460.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0940.211
X-RAY DIFFRACTIONr_mcbond_it2.51731386
X-RAY DIFFRACTIONr_mcbond_other0.5913542
X-RAY DIFFRACTIONr_mcangle_it3.44852126
X-RAY DIFFRACTIONr_scbond_it6.1218983
X-RAY DIFFRACTIONr_scangle_it7.99711873
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 121 -
Rwork0.179 2499 -
all-2620 -
obs--99.96 %
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)
10.895-0.498-0.14961.85980.53840.62760.1390.19440.0813-0.3167-0.10680.0389-0.1075-0.0981-0.03220.00330.0529-0.00110.00860.0298-0.080128.726942.008413.5327
21.0821-0.329-0.13711.42750.1680.6804-0.0186-0.09440.17550.0060.01590.0761-0.0299-0.05170.0027-0.0640.01010.0089-0.05030.0066-0.019921.878651.35329.2257
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
11-3 - 1209 - 132
22121 - 272133 - 284

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