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

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Basic information

Entry
Database: PDB / ID: 7xru
TitleDrimenyl diphosphate synthase D303E from Streptomyces showdoensis in complex with 2-fluorofarnesyl diphosphate (2F-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 / Chem-2CF / Drimenyl diphosphate synthase
Function and homology information
Biological speciesStreptomyces showdoensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 11, 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)55,5514
Polymers55,1021
Non-polymers4493
Water2,180121
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.350, 113.780, 179.810
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-2CF / (2E,6E)-2-fluoro-3,7,11-trimethyldodeca-2,6,10-trien-1-yl trihydrogen diphosphate


Mass: 400.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H27FO7P2 / 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.: 121 / 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: 49.17 %
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: 2.5→54.24 Å / Num. obs: 18064 / % possible obs: 97.1 % / Redundancy: 3.4 % / Biso Wilson estimate: 28.95 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.056 / Rrim(I) all: 0.107 / Net I/σ(I): 9.6 / Num. measured all: 61183 / Scaling rejects: 114
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
2.5-2.63.20.291667120560.9220.1820.3453.898.7
9.01-54.243.30.04413624190.9960.0270.05217.893.8

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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: 7XR7

7xr7


Resolution: 2.5→30.51 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2314 1805 10 %
Rwork0.1862 16244 -
obs0.1909 18049 96.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.35 Å2 / Biso mean: 31.7304 Å2 / Biso min: 14.49 Å2
Refinement stepCycle: final / Resolution: 2.5→30.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3705 0 51 121 3877
Biso mean--51.38 33.11 -
Num. residues----492
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.570.30961390.21861251139098
2.57-2.640.31181380.21171240137898
2.64-2.730.28331390.22421252139198
2.73-2.830.29691400.22381258139898
2.83-2.940.27911340.23591212134697
2.94-3.070.25861400.22021259139997
3.07-3.230.29831370.21581226136396
3.23-3.440.23841370.1981242137996
3.44-3.70.21611390.18371247138696
3.7-4.070.18351370.14361230136796
4.07-4.660.16581400.14351265140596
4.66-5.870.2291400.17421247138795
5.87-30.510.18851450.1711315146094
Refinement TLS params.Method: refined / Origin x: -18.1069 Å / Origin y: -5.0409 Å / Origin z: -21.2994 Å
111213212223313233
T0.1148 Å20.0119 Å20.0012 Å2-0.1768 Å20.0029 Å2--0.1807 Å2
L0.1059 °2-0.025 °20.1875 °2-0.8063 °20.3166 °2--1.0409 °2
S-0.0048 Å °0.0114 Å °0.048 Å °-0.0274 Å °0.022 Å °0.0253 Å °-0.067 Å °-0.066 Å °-0.0251 Å °
Refinement TLS groupSelection details: all

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