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- PDB-7xra: Drimenyl diphosphate synthase D303A from Streptomyces showdoensis... -

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Basic information

Entry
Database: PDB / ID: 7xra
TitleDrimenyl diphosphate synthase D303A 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: 1.95 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)55,4754
Polymers55,0441
Non-polymers4313
Water6,936385
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 area19160 Å2
Unit cell
Length a, b, c (Å)51.240, 113.620, 180.060
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 / Drimenyl diphosphate synthase


Mass: 55044.164 Da / Num. of mol.: 1 / Mutation: D303A
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.: 385 / 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: 2.42 Å3/Da / Density % sol: 49.11 %
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: 1.95→60.02 Å / Num. obs: 38605 / % possible obs: 99.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 19.84 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.07 / Rrim(I) all: 0.132 / Net I/σ(I): 7.7 / Num. measured all: 129439 / Scaling rejects: 16
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
1.95-23.30.558889826750.7620.3570.6652.299.9
8.94-60.022.50.03410574200.9980.0240.04214.493.4

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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: 1.95→30.42 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2221 1999 5.19 %
Rwork0.1771 36535 -
obs0.1794 38534 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.97 Å2 / Biso mean: 22.8243 Å2 / Biso min: 8.72 Å2
Refinement stepCycle: final / Resolution: 1.95→30.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3709 0 51 385 4145
Biso mean--33.34 28.24 -
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 (%)
1.95-20.24991400.207925702710100
2-2.050.27251410.19932575271699
2.05-2.110.21421420.176625792721100
2.11-2.180.22711410.17725862727100
2.18-2.260.21881420.176625892731100
2.26-2.350.23211420.174126022744100
2.35-2.460.22341420.18426102752100
2.46-2.590.25291440.185226162760100
2.59-2.750.26961410.199525792720100
2.75-2.960.27581430.20862631277499
2.96-3.260.24731430.19092612275599
3.26-3.730.18191430.15982617276099
3.73-4.690.17411460.142656280299
4.69-30.420.21341490.17882713286297
Refinement TLS params.Method: refined / Origin x: -18.0762 Å / Origin y: -5.203 Å / Origin z: -21.3925 Å
111213212223313233
T0.0564 Å20.0154 Å20.0049 Å2-0.0882 Å20.004 Å2--0.093 Å2
L0.1048 °2-0.0321 °20.044 °2-0.4001 °20.2269 °2--0.7419 °2
S0.0039 Å °0.0045 Å °0.0164 Å °0.0032 Å °0.0078 Å °-0.0032 Å °-0.0079 Å °-0.0456 Å °0.0038 Å °
Refinement TLS groupSelection details: all

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