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- PDB-7xr7: Drimenyl diphosphate synthase D303E from Streptomyces showdoensis... -

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Basic information

Entry
Database: PDB / ID: 7xr7
TitleDrimenyl diphosphate synthase D303E from Streptomyces showdoensis in complex with farnesyl diphosphate (FPP) and Mg2+
ComponentsSQHop_cyclase_C domain-containing protein
KeywordsBIOSYNTHETIC PROTEIN / Terpene synthases / type II TSs
Function / homologySqualene cyclase, C-terminal / Squalene-hopene cyclase C-terminal domain / Isomerases; Intramolecular transferases; Transferring other groups / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / isomerase activity / metal ion binding / FARNESYL DIPHOSPHATE / Drimenyl diphosphate synthase
Function and homology information
Biological speciesStreptomyces showdoensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsPan, X.M. / Du, W.Y. / Yang, Q. / Zhang, B. / Dong, L.B.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82073746 China
CitationJournal: J.Am.Chem.Soc. / Year: 2022
Title: Discovery, Structure, and Mechanism of a Class II Sesquiterpene Cyclase.
Authors: Pan, X. / Du, W. / Zhang, X. / Lin, X. / Li, F.R. / Yang, Q. / Wang, H. / Rudolf, J.D. / Zhang, B. / Dong, L.B.
History
DepositionMay 9, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 15, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SQHop_cyclase_C domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5334
Polymers55,1021
Non-polymers4313
Water8,971498
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-28 kcal/mol
Surface area19350 Å2
Unit cell
Length a, b, c (Å)51.640, 114.210, 180.670
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein SQHop_cyclase_C domain-containing protein


Mass: 55102.199 Da / Num. of mol.: 1 / Mutation: D303E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces showdoensis (bacteria) / Gene: VO63_21045 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2P2GK84
#2: Chemical ChemComp-FPP / FARNESYL DIPHOSPHATE


Mass: 382.326 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H28O7P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 498 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.45 Å3/Da / Density % sol: 49.88 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: HEPES, NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jan 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.63→57.1 Å / Num. obs: 66036 / % possible obs: 98.8 % / Redundancy: 3.3 % / Biso Wilson estimate: 16.56 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.049 / Rrim(I) all: 0.091 / Net I/σ(I): 11.1 / Num. measured all: 218692 / Scaling rejects: 190
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.63-1.663.50.6171137932790.7450.3750.7252.199.8
8.93-57.120.0387183670.9410.0360.05225.281.2

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Aimless0.7.7data scaling
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7XQZ

7xqz


Resolution: 1.63→35.43 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.26 / Phase error: 20.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2178 2000 3.03 %
Rwork0.1878 63991 -
obs0.1887 65991 98.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.65 Å2 / Biso mean: 23.4006 Å2 / Biso min: 9.06 Å2
Refinement stepCycle: final / Resolution: 1.63→35.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3713 0 51 498 4262
Biso mean--30.46 31.92 -
Num. residues----493
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.63-1.670.2671420.238445554697100
1.67-1.720.23151440.227345854729100
1.72-1.770.24531430.217945724715100
1.77-1.820.23461430.207745854728100
1.82-1.890.23121440.195445964740100
1.89-1.960.24211440.193246194763100
1.96-2.050.23741430.181245844727100
2.05-2.160.21671440.178546154759100
2.16-2.30.2361440.18344579472399
2.3-2.470.21031430.17844615475899
2.47-2.720.23031450.18814645479099
2.72-3.120.21081450.19834590473599
3.12-3.930.19621410.1774538467996
3.93-35.430.19851350.17644313444888
Refinement TLS params.Method: refined / Origin x: -18.1377 Å / Origin y: -5.0799 Å / Origin z: -21.3077 Å
111213212223313233
T0.0765 Å20.0268 Å2-0.0002 Å2-0.1207 Å20.0004 Å2--0.1164 Å2
L0.1427 °2-0.0327 °20.051 °2-0.8043 °20.4171 °2--1.1503 °2
S0.0194 Å °0.0125 Å °0.0407 Å °-0.0355 Å °-0.0146 Å °0.0041 Å °-0.0541 Å °-0.088 Å °-0.0124 Å °
Refinement TLS groupSelection details: all

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