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- PDB-8h4p: class I sesquiterpene synthase -

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Basic information

Entry
Database: PDB / ID: 8h4p
Titleclass I sesquiterpene synthase
ComponentsLongiborneol synthase CLM1
KeywordsSTRUCTURAL PROTEIN / class I sesquiterpene synthase
Function / homology
Function and homology information


carbon-oxygen lyase activity, acting on phosphates / Lyases; Carbon-oxygen lyases; Acting on phosphates / metal ion binding
Similarity search - Function
Trichodiene synthase / Trichodiene synthase (TRI5) / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
N-benzyl-N,N-diethylethanaminium / PYROPHOSPHATE / Longiborneol synthase CLM1
Similarity search - Component
Biological speciesGibberella zeae (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsLi, A.N. / Lou, T.T. / Ma, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22077007, 21877002 China
CitationJournal: J.Am.Chem.Soc. / Year: 2023
Title: Structural Insights into Three Sesquiterpene Synthases for the Biosynthesis of Tricyclic Sesquiterpenes and Chemical Space Expansion by Structure-Based Mutagenesis.
Authors: Lou, T. / Li, A. / Xu, H. / Pan, J. / Xing, B. / Wu, R. / Dickschat, J.S. / Yang, D. / Ma, M.
History
DepositionOct 11, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 23, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Longiborneol synthase CLM1
B: Longiborneol synthase CLM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,78712
Polymers77,9002
Non-polymers88610
Water16,844935
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6400 Å2
ΔGint-86 kcal/mol
Surface area22940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.704, 59.416, 83.548
Angle α, β, γ (deg.)90.000, 98.330, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Longiborneol synthase CLM1 / Culmorin biosynthesis protein 1 / Terpene cyclase CLM1


Mass: 38950.055 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gibberella zeae (strain ATCC MYA-4620 / CBS 123657 / FGSC 9075 / NRRL 31084 / PH-1) (fungus)
Strain: ATCC MYA-4620 / CBS 123657 / FGSC 9075 / NRRL 31084 / PH-1
Gene: CLM1, FG10397, FGRAMPH1_01T07999 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: I1S104, Lyases; Carbon-oxygen lyases; Acting on phosphates
#2: Chemical ChemComp-PPV / PYROPHOSPHATE


Mass: 177.975 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H4O7P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-BTM / N-benzyl-N,N-diethylethanaminium


Mass: 192.320 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H22N / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 935 / 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: 49.13 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium sulfate, 0.1 M BIS-TRIS, pH 7.0, 25% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Oct 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.47→30 Å / Num. obs: 124613 / % possible obs: 99.9 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 6.92
Reflection shellResolution: 1.47→1.5 Å / Rmerge(I) obs: 0.225 / Num. unique obs: 6111

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AF predict model

Resolution: 1.47→24.79 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.939 / SU B: 0.945 / SU ML: 0.037 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.067 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1975 6194 5 %RANDOM
Rwork0.1708 ---
obs0.1722 118394 98.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 48.97 Å2 / Biso mean: 10.656 Å2 / Biso min: 3.89 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å21.05 Å2
2---0.42 Å20 Å2
3----0.08 Å2
Refinement stepCycle: final / Resolution: 1.47→24.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5224 0 52 935 6211
Biso mean--11.79 21.48 -
Num. residues----652
LS refinement shellResolution: 1.471→1.509 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.216 440 -
Rwork0.187 8378 -
all-8818 -
obs--95.26 %

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