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- PDB-7xq4: Drimenyl diphosphate synthase from Streptomyces showdoensis (apo) -

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Basic information

Entry
Database: PDB / ID: 7xq4
TitleDrimenyl diphosphate synthase from Streptomyces showdoensis (apo)
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 / Drimenyl diphosphate synthase
Function and homology information
Biological speciesStreptomyces showdoensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 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 6, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 15, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: 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


Theoretical massNumber of molelcules
Total (without water)55,0881
Polymers55,0881
Non-polymers00
Water4,810267
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area19530 Å2
Unit cell
Length a, b, c (Å)51.180, 113.920, 179.670
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-846-

HOH

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Components

#1: Protein SQHop_cyclase_C domain-containing protein / Drimenyl diphosphate synthase


Mass: 55088.172 Da / Num. of mol.: 1
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.34 Å3/Da / Density % sol: 47.44 %
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: BL18U1 / Wavelength: 0.97916 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 1.58→56.96 Å / Num. obs: 70754 / % possible obs: 98.1 % / Redundancy: 6.5 % / Biso Wilson estimate: 14.56 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.029 / Rrim(I) all: 0.074 / Net I/σ(I): 16.2 / Num. measured all: 461347 / Scaling rejects: 311
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
1.58-1.616.60.3662267034490.9450.1530.3975.796.6
8.65-56.966.10.04830034930.9960.020.05228.499

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
PHASERphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: The starting model is predicted by Alphafold2

Resolution: 1.58→35.27 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1963 1999 2.83 %
Rwork0.1696 68733 -
obs0.1704 70732 97.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.42 Å2 / Biso mean: 19.0946 Å2 / Biso min: 7.36 Å2
Refinement stepCycle: final / Resolution: 1.58→35.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3676 0 0 267 3943
Biso mean---22.97 -
Num. residues----489
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 (%)
1.58-1.620.2191400.1974786492696
1.62-1.660.19981390.18184806494597
1.66-1.710.21971400.16564816495697
1.71-1.770.20291400.16184823496397
1.77-1.830.20741420.1554860500297
1.83-1.90.20281410.15954827496897
1.9-1.990.18911410.16934849499098
1.99-2.10.19241420.16194897503998
2.1-2.230.18231420.16114916505898
2.23-2.40.19831440.17084928507298
2.4-2.640.21371440.18124945508999
2.64-3.020.20121460.18735002514899
3.02-3.810.19751470.16545049519699
3.81-35.270.17851510.16455229538099
Refinement TLS params.Method: refined / Origin x: -17.5812 Å / Origin y: -5.2988 Å / Origin z: -21.4 Å
111213212223313233
T0.074 Å20.0126 Å20.0017 Å2-0.0807 Å20.0009 Å2--0.091 Å2
L0.1652 °2-0.0318 °20.12 °2-0.7606 °20.37 °2--1.1554 °2
S0.0197 Å °-0.0077 Å °0.0284 Å °-0.0044 Å °-0.0024 Å °0.0088 Å °-0.0283 Å °-0.0632 Å °-0.0201 Å °
Refinement TLS groupSelection details: all

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