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- PDB-4zq8: Crystal structure of a terpene synthase from Streptomyces lydicus... -

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Basic information

Entry
Database: PDB / ID: 4zq8
TitleCrystal structure of a terpene synthase from Streptomyces lydicus, target EFI-540129
ComponentsIsoprenoid Synthase
KeywordsTRANSFERASE / enzyme function initiative / EFI / Structural Genomics
Function / homology
Function and homology information


Lyases; Carbon-oxygen lyases; Acting on phosphates / lyase activity / metal ion binding
Similarity search - Function
Terpene cyclase-like 2 / Terpene synthase family 2, C-terminal metal binding / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesStreptomyces lydicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsToro, R. / Bhosle, R. / Vetting, M.W. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Washington, E. / Scott Glenn, A. ...Toro, R. / Bhosle, R. / Vetting, M.W. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hillerich, B. / Love, J. / Seidel, R.D. / Whalen, K.L. / Gerlt, J.A. / Poulter, C.D. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be published
Title: Crystal structure of a terpene synthase from Streptomyces lydicus, target EFI-540129
Authors: Toro, R. / Bhosle, R. / Vetting, M.W. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / ...Authors: Toro, R. / Bhosle, R. / Vetting, M.W. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hillerich, B. / Love, J. / Seidel, R.D. / Whalen, K.L. / Gerlt, J.A. / Poulter, C.D. / Almo, S.C. / Enzyme Function Initiative (EFI)
History
DepositionMay 8, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoprenoid Synthase
B: Isoprenoid Synthase


Theoretical massNumber of molelcules
Total (without water)83,9462
Polymers83,9462
Non-polymers00
Water12,484693
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-32 kcal/mol
Surface area25610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.737, 153.781, 155.179
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-634-

HOH

21A-682-

HOH

31A-736-

HOH

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Components

#1: Protein Isoprenoid Synthase


Mass: 41972.766 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lydicus (bacteria) / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0M3KL36*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 693 / 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: 2.3 Å3/Da / Density % sol: 46.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4
Details: Protein (43 mg/ml, 10 mM Hepes pH 7.5); Reservoir (0.1 M Bicine pH 9.0, 20% PEG 6000); cryo (20% glycerol)

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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 18, 2015 / 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→50 Å / Num. obs: 50304 / % possible obs: 93.8 % / Redundancy: 3 % / Biso Wilson estimate: 22.85 Å2 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.065 / Rrim(I) all: 0.123 / Χ2: 1.436 / Net I/av σ(I): 12.915 / Net I/σ(I): 6 / Num. measured all: 151695
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.033.10.48724830.8530.3070.580.69993.4
2.03-2.073.10.45924940.9040.2860.5450.77395
2.07-2.113.10.36225000.8630.2270.431.1294.2
2.11-2.153.10.35525210.9140.2230.4220.82894.3
2.15-2.23.10.34824440.9210.220.4140.80293.6
2.2-2.2530.38825230.9350.2480.4641.03594.5
2.25-2.3130.21425030.9420.1330.2541.61394.1
2.31-2.3730.26824870.9590.1680.3181.07194.3
2.37-2.4430.20725340.9590.1320.2471.07595.1
2.44-2.5230.17425110.9690.1110.2081.16494
2.52-2.6130.17825030.9640.1120.2121.25993.9
2.61-2.7130.1725190.970.1070.2021.47293.7
2.71-2.842.90.14324910.9750.0930.1721.61893.9
2.84-2.992.90.13725240.9760.0890.1651.95794
2.99-3.172.90.12224800.9770.080.1472.18293.1
3.17-3.422.90.10725170.9830.0690.1282.52293.2
3.42-3.762.90.08525310.9880.0550.1022.47193.5
3.76-4.313.10.06525480.9930.0410.0772.09793.5
4.31-5.433.20.04925640.9960.030.0581.81193.5
5.43-503.10.0426270.9960.0250.0481.3191.5

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LA6

4la6


Resolution: 2→25.843 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2538 2514 5.03 %
Rwork0.1933 47455 -
obs0.1963 49969 92.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.22 Å2 / Biso mean: 28.911 Å2 / Biso min: 9.69 Å2
Refinement stepCycle: final / Resolution: 2→25.843 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5069 0 0 694 5763
Biso mean---35.17 -
Num. residues----641
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075225
X-RAY DIFFRACTIONf_angle_d0.9987125
X-RAY DIFFRACTIONf_chiral_restr0.04758
X-RAY DIFFRACTIONf_plane_restr0.006953
X-RAY DIFFRACTIONf_dihedral_angle_d14.1451889
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 (%)
2-2.02090.30681160.23642237235379
2.0209-2.06220.29781440.22482644278895
2.0622-2.1070.30961410.25172640278194
2.107-2.1560.27351310.21542680281194
2.156-2.20990.34141410.27322593273493
2.2099-2.26960.46261390.37912581272092
2.2696-2.33630.47251270.29632541266889
2.3363-2.41170.27161270.20152694282195
2.4117-2.49780.28141470.19572649279694
2.4978-2.59770.25651480.19492678282694
2.5977-2.71580.291360.18962669280594
2.7158-2.85880.31641370.19822640277794
2.8588-3.03770.25131490.20042683283294
3.0377-3.27180.24141500.18862658280893
3.2718-3.60030.24771440.18442651279592
3.6003-4.11940.20351500.15752693284394
4.1194-5.18320.17121460.13232723286994
5.1832-25.8450.1791410.14612801294293
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)
10.72350.32290.46471.4335-0.29071.677-0.0520.04390.28930.00380.06770.209-0.2288-0.0326-0.0210.22670.01710.01250.12780.02790.2435-25.0394-6.268813.3979
21.4371-0.5161-1.23640.67160.59233.20910.1083-0.14930.10150.0236-0.0028-0.0442-0.2016-0.1842-0.06820.1631-0.0096-0.00520.208-0.00450.1808-34.9677-27.446421.8054
30.34320.1956-0.10380.64180.081.1668-0.02050.01430.0533-0.07940.0190.0111-0.06660.04720.00210.13690.01440.00370.176-0.00020.1726-22.5006-23.439816.273
40.5530.1034-0.09831.09130.07023.02270.0396-0.01210.11590.02590.0663-0.0074-0.28270.1216-0.1030.167-0.026-0.01450.1777-0.00310.218-10.4111-10.983425.5692
54.48860.33461.73651.12240.54371.44160.17860.0979-0.68660.14150.0766-0.28560.41230.1709-0.1880.36470.065-0.06620.2074-0.00290.3262-15.3582-58.139715.7951
60.9718-0.3225-0.12870.990.22081.7056-0.0266-0.2123-0.26860.25770.0159-0.09330.51540.33850.01350.26670.0316-0.03260.2030.0140.2571-13.0629-51.133521.1493
70.8254-0.0375-0.27080.28120.20640.935-0.0266-0.0457-0.0120.06710.0241-0.08040.11610.08160.00140.17310.0073-0.0120.1873-0.00970.1704-17.6612-36.087821.7585
81.84990.5846-1.42421.2086-0.38132.2314-0.12180.159-0.1360.07640.05360.04580.253-0.21410.06570.18-0.025-0.01150.1802-0.03370.1796-35.3481-46.975613.1893
92.61680.6378-0.49931.5165-0.04391.2175-0.0046-0.301-0.34090.1127-0.1138-0.07470.31560.0950.10570.2553-0.01050.0010.169-0.01130.217-25.7329-53.808710.6399
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and (resid 29 through 111 )A0
2X-RAY DIFFRACTION2chain A and (resid 112 through 142 )A0
3X-RAY DIFFRACTION3chain A and (resid 143 through 241 )A0
4X-RAY DIFFRACTION4chain A and (resid 242 through 352 )A0
5X-RAY DIFFRACTION5chain B and (resid 28 through 60 )B0
6X-RAY DIFFRACTION6chain B and (resid 61 through 111 )B0
7X-RAY DIFFRACTION7chain B and (resid 112 through 241 )B0
8X-RAY DIFFRACTION8chain B and (resid 242 through 317 )B0
9X-RAY DIFFRACTION9chain B and (resid 318 through 352 )B0

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