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

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Basic information

Entry
Database: PDB / ID: 5ygj
TitleCrystal structure of a synthase from Streptomyces sp. CL190
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 / Cyclolavandulyl diphosphate synthase
Function and homology information
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.648 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 1.1Dec 25, 2019Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)97,5104
Polymers97,5104
Non-polymers00
Water63135
1
A: Cyclolavandulyl diphosphate synthase
C: Cyclolavandulyl diphosphate synthase


Theoretical massNumber of molelcules
Total (without water)48,7552
Polymers48,7552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-21 kcal/mol
Surface area17910 Å2
MethodPISA
2
B: Cyclolavandulyl diphosphate synthase
D: Cyclolavandulyl diphosphate synthase


Theoretical massNumber of molelcules
Total (without water)48,7552
Polymers48,7552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-20 kcal/mol
Surface area17740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.525, 118.436, 88.872
Angle α, β, γ (deg.)90.00, 116.35, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-308-

HOH

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Components

#1: Protein
Cyclolavandulyl diphosphate synthase


Mass: 24377.596 Da / Num. of mol.: 4
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.24 Å3/Da / Density % sol: 45.03 % / Mosaicity: 0.911 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: NaAc, HEPES, PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 16, 2017
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.648→25 Å / Num. obs: 24803 / % possible obs: 99.1 % / Redundancy: 3.5 % / Biso Wilson estimate: 61.98 Å2 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.033 / Rrim(I) all: 0.063 / Χ2: 1.574 / Net I/σ(I): 17.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.65-2.743.40.36424160.9240.2270.4291.47796.3
2.74-2.853.50.30324670.9460.1880.3571.45999.7
2.85-2.983.50.21624870.9740.1340.2551.54499.9
2.98-3.143.50.16225030.9830.1010.1911.60799.8
3.14-3.343.50.10224740.9910.0630.1211.72499.8
3.34-3.593.50.06725030.9950.0420.0791.8299.9
3.59-3.953.50.05224850.9970.0330.0621.81199.8
3.95-4.523.50.04724770.9950.030.0561.66999.2
4.52-5.693.40.04424820.9960.0290.0531.39698.7
5.69-253.40.03125090.9990.020.0371.20198.4

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Phasing

PhasingMethod: molecular replacement

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Processing

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

5xk3


Resolution: 2.648→24.912 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2685 1258 5.08 %
Rwork0.2092 --
obs0.2122 24781 99.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.648→24.912 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6477 0 0 35 6512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126621
X-RAY DIFFRACTIONf_angle_d1.6918952
X-RAY DIFFRACTIONf_dihedral_angle_d16.313958
X-RAY DIFFRACTIONf_chiral_restr0.089987
X-RAY DIFFRACTIONf_plane_restr0.011156
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6476-2.75350.4261330.32232534X-RAY DIFFRACTION96
2.7535-2.87870.36911420.27712622X-RAY DIFFRACTION100
2.8787-3.03020.37141430.26132612X-RAY DIFFRACTION100
3.0302-3.21970.32291440.26972622X-RAY DIFFRACTION100
3.2197-3.46760.36371410.22852611X-RAY DIFFRACTION100
3.4676-3.81550.27461490.20542633X-RAY DIFFRACTION100
3.8155-4.3650.22711490.19012613X-RAY DIFFRACTION99
4.365-5.48980.20631300.17672619X-RAY DIFFRACTION99
5.4898-24.91320.22951270.19052657X-RAY DIFFRACTION98

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