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- PDB-4kk2: Crystal structure of a chimeric FPP/GFPP synthase (TARGET EFI-502... -

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Entry
Database: PDB / ID: 4kk2
TitleCrystal structure of a chimeric FPP/GFPP synthase (TARGET EFI-502313c) from Artemisia spiciformiS (1-72:GI751454468,73-346:GI75233326), apo structure
ComponentsMonoterpene synthase FDS-5, chloroplastic - Farnesyl diphosphate synthase 1 chimera
KeywordsTRANSFERASE / ISOPRENOID SYNTHASE / ENZYME FUNCTION INITIATIVE / Structural Genomics
Function / homology
Function and homology information


chrysanthemyl diphosphate synthase / lavandulyl diphosphate synthase / chrysanthemyl diphosphate synthase activity / lavandulyl diphosphate synthase activity / geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / (2E,6E)-farnesyl diphosphate synthase / isoprenoid biosynthetic process / farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity ...chrysanthemyl diphosphate synthase / lavandulyl diphosphate synthase / chrysanthemyl diphosphate synthase activity / lavandulyl diphosphate synthase activity / geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / (2E,6E)-farnesyl diphosphate synthase / isoprenoid biosynthetic process / farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / geranyltranstransferase activity / chloroplast / metal ion binding
Similarity search - Function
Farnesyl pyrophosphate synthase-like / 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
Monoterpene synthase FDS-5, chloroplastic / Farnesyl diphosphate synthase 1
Similarity search - Component
Biological speciesArtemisia spiciformis (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsVetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Hillerich, B. ...Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Poulter, C.D. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be Published
Title: Crystal structure of a chimeric FPP/GFPP synthase (TARGET EFI-502313c) from Artemisia spiciformis (1-72:GI751454468,73-346:GI75233326), apo structure
Authors: Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. ...Authors: Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Poulter, C.D. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
History
DepositionMay 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Jan 31, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Monoterpene synthase FDS-5, chloroplastic - Farnesyl diphosphate synthase 1 chimera
B: Monoterpene synthase FDS-5, chloroplastic - Farnesyl diphosphate synthase 1 chimera


Theoretical massNumber of molelcules
Total (without water)84,3042
Polymers84,3042
Non-polymers00
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-35 kcal/mol
Surface area28700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.145, 122.145, 114.282
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Detailsbiological unit is a dimer

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Components

#1: Protein Monoterpene synthase FDS-5, chloroplastic - Farnesyl diphosphate synthase 1 chimera / Chrysanthemyl diphosphate synthase / CPP synthase / Dimethylallyltranstransferase / Lavandulyl ...Chrysanthemyl diphosphate synthase / CPP synthase / Dimethylallyltranstransferase / Lavandulyl diphosphate synthase / LPP synthase / Dimethylallyltranstransferase / (2E / 6E)-farnesyl diphosphate synthase


Mass: 42152.074 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Artemisia spiciformis (plant) / Gene: FDS-5, FDS-1 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q7XYS8, UniProt: Q7XYS9, chrysanthemyl diphosphate synthase, dimethylallyltranstransferase, lavandulyl diphosphate synthase, (2E,6E)-farnesyl diphosphate synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 2.92 Å3/Da / Density % sol: 57.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein (10 mM Hepes pH 7.5, 150 mM NaCl, 10% glycerol, 1 mM DTT, 5 mM MgCl), Reservoir (0.09 M HEPES pH 7.5, 1.26 M Sodium Citrate, 10% glycerol), Cryoprotection (Reservoir, + 20% glycerol) ...Details: Protein (10 mM Hepes pH 7.5, 150 mM NaCl, 10% glycerol, 1 mM DTT, 5 mM MgCl), Reservoir (0.09 M HEPES pH 7.5, 1.26 M Sodium Citrate, 10% glycerol), Cryoprotection (Reservoir, + 20% glycerol), VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Mar 15, 2012 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.2→105.781 Å / Num. all: 49118 / Num. obs: 49118 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.4 % / Biso Wilson estimate: 36.95 Å2 / Rmerge(I) obs: 0.117 / Rsym value: 0.117 / Net I/σ(I): 14.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.2-2.3211.30.8550.98064271490.855100
2.32-2.4611.30.5651.47697067950.565100
2.46-2.6311.40.3672.17210363250.367100
2.63-2.8411.50.2353.36849759630.235100
2.84-3.1111.50.1425.36268854390.142100
3.11-3.4811.50.0996.75713349490.099100
3.48-4.0211.60.1045.85013943400.104100
4.02-4.9211.50.0916.64299337260.091100
4.92-6.9611.50.05110.93292128630.051100
6.96-37.73910.70.02821.91686015690.02897.5

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FPS

1fps


Resolution: 2.2→37.739 Å / Occupancy max: 1 / Occupancy min: 0.37 / FOM work R set: 0.8916 / SU ML: 0.2 / σ(F): 0 / σ(I): 0 / Phase error: 18.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1985 2482 5.06 %RANDOM
Rwork0.1568 ---
all0.1588 49073 --
obs0.1588 49073 99.93 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 127.44 Å2 / Biso mean: 42.9078 Å2 / Biso min: 12.76 Å2
Refinement stepCycle: LAST / Resolution: 2.2→37.739 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5497 0 0 219 5716
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075634
X-RAY DIFFRACTIONf_angle_d0.9917619
X-RAY DIFFRACTIONf_chiral_restr0.064836
X-RAY DIFFRACTIONf_plane_restr0.004965
X-RAY DIFFRACTIONf_dihedral_angle_d14.5732089
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.24230.26271530.211125732726100
2.2423-2.28810.26431570.192525952752100
2.2881-2.33780.24021470.182425332680100
2.3378-2.39220.23731700.183425562726100
2.3922-2.4520.22521330.172625872720100
2.452-2.51830.20781490.169925602709100
2.5183-2.59240.19731340.158925772711100
2.5924-2.6760.2071250.153325932718100
2.676-2.77170.17651230.154626002723100
2.7717-2.88260.20951460.152225912737100
2.8826-3.01370.21821230.162225742697100
3.0137-3.17260.22321250.153626262751100
3.1726-3.37120.1891320.156226012733100
3.3712-3.63130.20531480.14925712719100
3.6313-3.99640.15311330.138925972730100
3.9964-4.57380.1631120.13326312743100
4.5738-5.75920.20251290.154626272756100
5.7592-37.7440.19331430.17232599274299
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)
11.62760.5485-0.17721.29240.00272.08190.0432-0.12170.41960.0545-0.03370.3162-0.5451-0.1610.02780.2930.08990.03140.1749-0.02950.346334.598440.712240.7436
22.5834-0.4633-1.23811.6908-0.04642.262-0.2998-0.6138-0.4392-0.01960.2013-0.08770.29140.31550.03630.27160.1081-0.02120.3121-0.00280.239134.24130.389162.2098
32.19510.1205-1.34753.9806-0.3951.9770.2313-1.11940.44820.6858-0.04620.4364-0.35180.4303-0.11880.42810.0741-0.02760.6819-0.10810.330734.297539.228869.8993
42.02810.5352-0.59962.0524-0.49222.1318-0.0716-0.2435-0.30110.0931-0.0668-0.13970.5420.45250.09620.26830.0838-0.02450.24780.03730.241451.352417.228444.1945
51.35290.6356-0.30621.1181-0.18911.8633-0.0587-0.0231-0.2439-0.1365-0.0612-0.13250.13050.39550.08360.27720.0763-0.01940.24510.02990.212555.095322.528629.8498
61.97120.872-0.50812.143-0.5172.21960.0091-0.06710.0516-0.0578-0.08620.26190.16080.10320.08380.2070.0596-0.0010.14710.01390.15543.639821.339939.2129
71.4904-0.16450.44451.41240.1591.9995-0.01910.1330.1156-0.2467-0.06080.4115-0.101-0.19490.05660.21950.0507-0.05510.14670.00860.207137.299430.613923.4251
82.2270.4775-0.26312.1936-0.73011.58560.09180.00710.1579-0.0332-0.0726-0.0352-0.21080.36090.08820.2280.01050.00310.23920.05080.147757.414733.905323.6362
93.32373.18350.94055.44981.57921.055-0.20780.1867-0.0775-0.12590.2490.35350.22620.10260.00430.37110.0388-0.01970.24810.05830.264443.734923.697113.5239
101.6597-0.99920.88493.6458-1.08811.5463-0.1745-0.6136-0.4532-0.46510.35260.46580.3157-0.3838-0.1060.44870.02150.00420.34290.08860.498832.697311.899617.0814
113.1372-1.25270.81150.9710.68772.3996-0.30060.46680.1446-0.612-0.06841.37850.0567-0.89390.31240.46090.0188-0.27060.5775-0.02020.72122.704619.4717.967
126.71451.60810.52032.21190.74051.0848-0.6091.3621-0.4925-0.90060.43850.39890.2158-0.06540.18560.5738-0.1003-0.09530.3673-0.03650.405837.704818.72414.868
132.94830.9571-0.23954.2998-0.90413.0023-0.34050.1773-0.8769-0.5710.0703-0.14560.86890.2230.15150.47280.03360.09750.28960.01480.316255.627923.132112.3143
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 9:173)A9 - 173
2X-RAY DIFFRACTION2chain 'A' and (resseq 174:287)A174 - 287
3X-RAY DIFFRACTION3chain 'A' and (resseq 288:343)A288 - 343
4X-RAY DIFFRACTION4chain 'B' and (resseq 10:53)B10 - 53
5X-RAY DIFFRACTION5chain 'B' and (resseq 54:100)B54 - 100
6X-RAY DIFFRACTION6chain 'B' and (resseq 101:146)B101 - 146
7X-RAY DIFFRACTION7chain 'B' and (resseq 147:199)B147 - 199
8X-RAY DIFFRACTION8chain 'B' and (resseq 200:218)B200 - 218
9X-RAY DIFFRACTION9chain 'B' and (resseq 219:242)B219 - 242
10X-RAY DIFFRACTION10chain 'B' and (resseq 243:261)B243 - 261
11X-RAY DIFFRACTION11chain 'B' and (resseq 262:287)B262 - 287
12X-RAY DIFFRACTION12chain 'B' and (resseq 288:323)B288 - 323
13X-RAY DIFFRACTION13chain 'B' and (resseq 324:346)B324 - 346

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