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- PDB-5ygk: Crystal structure of a synthase from Streptomyces sp. CL190 with ... -

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Basic information

Entry
Database: PDB / ID: 5ygk
TitleCrystal structure of a synthase from Streptomyces sp. CL190 with dmaspp
ComponentsCyclolavandulyl diphosphate synthase
KeywordsBIOSYNTHETIC PROTEIN / substrate binding / Cyclolavandulyl diphosphate synthase / inhibitor
Function / homologyditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl diphosphate specific] activity / Decaprenyl diphosphate synthase-like / Putative undecaprenyl diphosphate synthase / polyprenol biosynthetic process / Decaprenyl diphosphate synthase-like superfamily / metal ion binding / DIMETHYLALLYL S-THIOLODIPHOSPHATE / Cyclolavandulyl diphosphate synthase
Function and homology information
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.047 Å
AuthorsGao, J. / Liu, W.D. / Chen, C.C. / Guo, R.T.
CitationJournal: Acs Catalysis / Year: 2018
Title: Catalytic Role of Conserved Asparagine, Glutamine, Serine, and Tyrosine Residues in Isoprenoid Biosynthesis Enzymes.
Authors: Malwal, S.R. / Gao, J. / Hu, X. / Yang, Y. / Liu, W. / Huang, J.W. / Ko, T.P. / Li, L. / Chen, C.C. / O'Dowd, B. / Khade, R.L. / Zhang, Y. / Zhang, Y. / Oldfield, E. / Guo, R.T.
History
DepositionSep 23, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 2.0Oct 16, 2019Group: Data collection / Non-polymer description / Structure summary
Category: chem_comp / entity
Item: _chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight
Revision 2.1Dec 25, 2019Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 2.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyclolavandulyl diphosphate synthase
B: Cyclolavandulyl diphosphate synthase
C: Cyclolavandulyl diphosphate synthase
D: Cyclolavandulyl diphosphate synthase
E: Cyclolavandulyl diphosphate synthase
F: Cyclolavandulyl diphosphate synthase
G: Cyclolavandulyl diphosphate synthase
H: Cyclolavandulyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,41032
Polymers195,0218
Non-polymers4,38924
Water15,331851
1
A: Cyclolavandulyl diphosphate synthase
E: Cyclolavandulyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8528
Polymers48,7552
Non-polymers1,0976
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5090 Å2
ΔGint-50 kcal/mol
Surface area17210 Å2
MethodPISA
2
B: Cyclolavandulyl diphosphate synthase
F: Cyclolavandulyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8528
Polymers48,7552
Non-polymers1,0976
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5250 Å2
ΔGint-47 kcal/mol
Surface area16970 Å2
MethodPISA
3
C: Cyclolavandulyl diphosphate synthase
H: Cyclolavandulyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8528
Polymers48,7552
Non-polymers1,0976
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6110 Å2
ΔGint-48 kcal/mol
Surface area17410 Å2
MethodPISA
4
D: Cyclolavandulyl diphosphate synthase
G: Cyclolavandulyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8528
Polymers48,7552
Non-polymers1,0976
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5160 Å2
ΔGint-48 kcal/mol
Surface area16860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.090, 119.308, 93.133
Angle α, β, γ (deg.)90.000, 117.350, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 3:11 or resseq 13:22 or (resid...
21(chain B and (resseq 3:11 or resseq 13:22 or (resid...
31(chain C and (resseq 3:11 or resseq 13:22 or (resid...
41(chain D and (resseq 3:11 or resseq 13:22 or (resid...
51(chain E and (resseq 3:11 or resseq 13:22 or (resid...
61(chain F and (resseq 3:11 or resseq 13:22 or (resid...
71(chain G and (resseq 3:11 or resseq 13:22 or (resid...
81(chain H and (resseq 3:11 or resseq 13:22 or (resid...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRMETMET(chain A and (resseq 3:11 or resseq 13:22 or (resid...AA3 - 113 - 11
12ARGARGLEULEU(chain A and (resseq 3:11 or resseq 13:22 or (resid...AA13 - 2213 - 22
13ASPASPASPASP(chain A and (resseq 3:11 or resseq 13:22 or (resid...AA2323
14METMETARGARG(chain A and (resseq 3:11 or resseq 13:22 or (resid...AA1 - 2101 - 210
15METMETARGARG(chain A and (resseq 3:11 or resseq 13:22 or (resid...AA1 - 2101 - 210
16METMETARGARG(chain A and (resseq 3:11 or resseq 13:22 or (resid...AA1 - 2101 - 210
17METMETARGARG(chain A and (resseq 3:11 or resseq 13:22 or (resid...AA1 - 2101 - 210
18METMETARGARG(chain A and (resseq 3:11 or resseq 13:22 or (resid...AA1 - 2101 - 210
19METMETARGARG(chain A and (resseq 3:11 or resseq 13:22 or (resid...AA1 - 2101 - 210
21THRTHRMETMET(chain B and (resseq 3:11 or resseq 13:22 or (resid...BB3 - 113 - 11
22ARGARGLEULEU(chain B and (resseq 3:11 or resseq 13:22 or (resid...BB13 - 2213 - 22
23ASPASPASPASP(chain B and (resseq 3:11 or resseq 13:22 or (resid...BB2323
24METMETARGARG(chain B and (resseq 3:11 or resseq 13:22 or (resid...BB1 - 2081 - 208
25METMETARGARG(chain B and (resseq 3:11 or resseq 13:22 or (resid...BB1 - 2081 - 208
26METMETARGARG(chain B and (resseq 3:11 or resseq 13:22 or (resid...BB1 - 2081 - 208
27METMETARGARG(chain B and (resseq 3:11 or resseq 13:22 or (resid...BB1 - 2081 - 208
28METMETARGARG(chain B and (resseq 3:11 or resseq 13:22 or (resid...BB1 - 2081 - 208
29METMETARGARG(chain B and (resseq 3:11 or resseq 13:22 or (resid...BB1 - 2081 - 208
31THRTHRMETMET(chain C and (resseq 3:11 or resseq 13:22 or (resid...CC3 - 113 - 11
32ARGARGLEULEU(chain C and (resseq 3:11 or resseq 13:22 or (resid...CC13 - 2213 - 22
33ASPASPASPASP(chain C and (resseq 3:11 or resseq 13:22 or (resid...CC2323
34METMETALAALA(chain C and (resseq 3:11 or resseq 13:22 or (resid...CC1 - 2171 - 217
35METMETALAALA(chain C and (resseq 3:11 or resseq 13:22 or (resid...CC1 - 2171 - 217
36METMETALAALA(chain C and (resseq 3:11 or resseq 13:22 or (resid...CC1 - 2171 - 217
37METMETALAALA(chain C and (resseq 3:11 or resseq 13:22 or (resid...CC1 - 2171 - 217
38METMETALAALA(chain C and (resseq 3:11 or resseq 13:22 or (resid...CC1 - 2171 - 217
39METMETALAALA(chain C and (resseq 3:11 or resseq 13:22 or (resid...CC1 - 2171 - 217
41THRTHRMETMET(chain D and (resseq 3:11 or resseq 13:22 or (resid...DD3 - 113 - 11
42ARGARGLEULEU(chain D and (resseq 3:11 or resseq 13:22 or (resid...DD13 - 2213 - 22
43ASPASPASPASP(chain D and (resseq 3:11 or resseq 13:22 or (resid...DD2323
44METMETARGARG(chain D and (resseq 3:11 or resseq 13:22 or (resid...DD1 - 2081 - 208
45METMETARGARG(chain D and (resseq 3:11 or resseq 13:22 or (resid...DD1 - 2081 - 208
46METMETARGARG(chain D and (resseq 3:11 or resseq 13:22 or (resid...DD1 - 2081 - 208
47METMETARGARG(chain D and (resseq 3:11 or resseq 13:22 or (resid...DD1 - 2081 - 208
48METMETARGARG(chain D and (resseq 3:11 or resseq 13:22 or (resid...DD1 - 2081 - 208
49METMETARGARG(chain D and (resseq 3:11 or resseq 13:22 or (resid...DD1 - 2081 - 208
51THRTHRMETMET(chain E and (resseq 3:11 or resseq 13:22 or (resid...EE3 - 113 - 11
52ARGARGLEULEU(chain E and (resseq 3:11 or resseq 13:22 or (resid...EE13 - 2213 - 22
53ASPASPASPASP(chain E and (resseq 3:11 or resseq 13:22 or (resid...EE2323
54METMETARGARG(chain E and (resseq 3:11 or resseq 13:22 or (resid...EE1 - 2081 - 208
55METMETARGARG(chain E and (resseq 3:11 or resseq 13:22 or (resid...EE1 - 2081 - 208
56METMETARGARG(chain E and (resseq 3:11 or resseq 13:22 or (resid...EE1 - 2081 - 208
57METMETARGARG(chain E and (resseq 3:11 or resseq 13:22 or (resid...EE1 - 2081 - 208
58METMETARGARG(chain E and (resseq 3:11 or resseq 13:22 or (resid...EE1 - 2081 - 208
59METMETARGARG(chain E and (resseq 3:11 or resseq 13:22 or (resid...EE1 - 2081 - 208
61THRTHRMETMET(chain F and (resseq 3:11 or resseq 13:22 or (resid...FF3 - 113 - 11
62ARGARGLEULEU(chain F and (resseq 3:11 or resseq 13:22 or (resid...FF13 - 2213 - 22
63ASPASPASPASP(chain F and (resseq 3:11 or resseq 13:22 or (resid...FF2323
64THRTHRASPASP(chain F and (resseq 3:11 or resseq 13:22 or (resid...FF2 - 2092 - 209
65THRTHRASPASP(chain F and (resseq 3:11 or resseq 13:22 or (resid...FF2 - 2092 - 209
66THRTHRASPASP(chain F and (resseq 3:11 or resseq 13:22 or (resid...FF2 - 2092 - 209
67THRTHRASPASP(chain F and (resseq 3:11 or resseq 13:22 or (resid...FF2 - 2092 - 209
68THRTHRASPASP(chain F and (resseq 3:11 or resseq 13:22 or (resid...FF2 - 2092 - 209
69THRTHRASPASP(chain F and (resseq 3:11 or resseq 13:22 or (resid...FF2 - 2092 - 209
71THRTHRMETMET(chain G and (resseq 3:11 or resseq 13:22 or (resid...GG3 - 113 - 11
72ARGARGLEULEU(chain G and (resseq 3:11 or resseq 13:22 or (resid...GG13 - 2213 - 22
73ASPASPASPASP(chain G and (resseq 3:11 or resseq 13:22 or (resid...GG2323
74THRTHRASPASP(chain G and (resseq 3:11 or resseq 13:22 or (resid...GG2 - 2092 - 209
75THRTHRASPASP(chain G and (resseq 3:11 or resseq 13:22 or (resid...GG2 - 2092 - 209
76THRTHRASPASP(chain G and (resseq 3:11 or resseq 13:22 or (resid...GG2 - 2092 - 209
77THRTHRASPASP(chain G and (resseq 3:11 or resseq 13:22 or (resid...GG2 - 2092 - 209
78THRTHRASPASP(chain G and (resseq 3:11 or resseq 13:22 or (resid...GG2 - 2092 - 209
79THRTHRASPASP(chain G and (resseq 3:11 or resseq 13:22 or (resid...GG2 - 2092 - 209
81THRTHRMETMET(chain H and (resseq 3:11 or resseq 13:22 or (resid...HH3 - 113 - 11
82ARGARGLEULEU(chain H and (resseq 3:11 or resseq 13:22 or (resid...HH13 - 2213 - 22
83ASPASPASPASP(chain H and (resseq 3:11 or resseq 13:22 or (resid...HH2323
84THRTHRALAALA(chain H and (resseq 3:11 or resseq 13:22 or (resid...HH2 - 2172 - 217
85THRTHRALAALA(chain H and (resseq 3:11 or resseq 13:22 or (resid...HH2 - 2172 - 217
86THRTHRALAALA(chain H and (resseq 3:11 or resseq 13:22 or (resid...HH2 - 2172 - 217
87THRTHRALAALA(chain H and (resseq 3:11 or resseq 13:22 or (resid...HH2 - 2172 - 217
88THRTHRALAALA(chain H and (resseq 3:11 or resseq 13:22 or (resid...HH2 - 2172 - 217
89THRTHRALAALA(chain H and (resseq 3:11 or resseq 13:22 or (resid...HH2 - 2172 - 217

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Components

#1: Protein
Cyclolavandulyl diphosphate synthase


Mass: 24377.596 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. (strain CL190) (bacteria)
Strain: CL190 / Plasmid: pET46Ek/LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: X5IYJ5
#2: Chemical
ChemComp-DST / DIMETHYLALLYL S-THIOLODIPHOSPHATE / DMASPP / DMAPP / DMADP / Dimethylallyl pyrophosphate / dimethylallyl diphosphate / isoprenyl pyrophosphate


Mass: 262.158 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C5H12O6P2S
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 851 / 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: 2.28 Å3/Da / Density % sol: 46.04 % / Mosaicity: 0.909 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: NaAc, NaCl HEPES, PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.9998 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Sep 10, 2017
RadiationMonochromator: LN2 cooled Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 2.047→25 Å / Num. obs: 109264 / % possible obs: 99.7 % / Redundancy: 5.3 % / Biso Wilson estimate: 34.08 Å2 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.026 / Rrim(I) all: 0.061 / Χ2: 0.784 / Net I/σ(I): 9.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.05-2.1250.499108000.8920.2360.5540.48799
2.12-2.215.30.337108620.9510.1580.3730.51299.7
2.21-2.315.40.263108770.9680.1230.290.52999.7
2.31-2.435.40.186109030.9820.0870.2060.56699.8
2.43-2.585.40.129109250.990.060.1420.64399.8
2.58-2.785.40.094109060.9940.0440.1040.698100
2.78-3.065.40.064109640.9970.030.0710.809100
3.06-3.55.30.046109570.9980.0220.0511.096100
3.5-4.415.30.036109970.9990.0170.041.252100
4.41-255.30.032110730.9990.0150.0351.21799.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
PHENIX(1.10_2155: ???)refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XK3

5xk3


Resolution: 2.047→24.866 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.12
RfactorNum. reflection% reflection
Rfree0.2357 2004 1.84 %
Rwork0.1844 --
obs0.1853 109181 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 112.4 Å2 / Biso mean: 41.8314 Å2 / Biso min: 14.65 Å2
Refinement stepCycle: final / Resolution: 2.047→24.866 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13262 0 232 851 14345
Biso mean--47.87 42.91 -
Num. residues----1683
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00913783
X-RAY DIFFRACTIONf_angle_d1.44518648
X-RAY DIFFRACTIONf_chiral_restr0.0632009
X-RAY DIFFRACTIONf_plane_restr0.0072392
X-RAY DIFFRACTIONf_dihedral_angle_d18.3758193
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6970X-RAY DIFFRACTION10.432TORSIONAL
12B6970X-RAY DIFFRACTION10.432TORSIONAL
13C6970X-RAY DIFFRACTION10.432TORSIONAL
14D6970X-RAY DIFFRACTION10.432TORSIONAL
15E6970X-RAY DIFFRACTION10.432TORSIONAL
16F6970X-RAY DIFFRACTION10.432TORSIONAL
17G6970X-RAY DIFFRACTION10.432TORSIONAL
18H6970X-RAY DIFFRACTION10.432TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0473-2.12040.30231960.2486103361053296
2.1204-2.20530.27842090.22371068910898100
2.2053-2.30560.23751950.21751068910884100
2.3056-2.4270.27781880.21561074610934100
2.427-2.57890.27331880.20941076710955100
2.5789-2.77780.26171940.21881073510929100
2.7778-3.05690.26592160.22221078210998100
3.0569-3.49820.27322160.19131076610982100
3.4982-4.40340.17952040.15341081811022100
4.4034-24.86820.20241980.1461108491104799

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