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- PDB-7xkx: Crystal structure of Tpn2 -

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Basic information

Entry
Database: PDB / ID: 7xkx
TitleCrystal structure of Tpn2
ComponentsSQHop_cyclase_C domain-containing protein
KeywordsBIOSYNTHETIC PROTEIN / Tpn2 / terpene synthase / terpentecin / bacterial TS
Function / homology
Function and homology information


diterpenoid biosynthetic process / terpene synthase activity / magnesium ion binding
Similarity search - Function
Glycosyltransferase - #160 / Squalene cyclase, C-terminal / Squalene-hopene cyclase C-terminal domain / : / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
Squalene cyclase C-terminal domain-containing protein
Similarity search - Component
Biological speciesKitasatospora sp. CB02891 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 Å
AuthorsChang, C.Y. / Stowell, E.A. / Lin, Y.L. / Ehrenberger, M.A. / Rudolf, J.D.
Funding support Taiwan, United States, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)110-2113-M-A49-026-MY3 Taiwan
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R00 GM124461 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM142574 United States
CitationJournal: Commun Chem / Year: 2022
Title: Structure-guided product determination of the bacterial type II diterpene synthase Tpn2.
Authors: Stowell, E.A. / Ehrenberger, M.A. / Lin, Y.L. / Chang, C.Y. / Rudolf, J.D.
History
DepositionApr 20, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 1, 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
B: SQHop_cyclase_C domain-containing protein


Theoretical massNumber of molelcules
Total (without water)116,0432
Polymers116,0432
Non-polymers00
Water2,882160
1
A: SQHop_cyclase_C domain-containing protein


Theoretical massNumber of molelcules
Total (without water)58,0221
Polymers58,0221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SQHop_cyclase_C domain-containing protein


Theoretical massNumber of molelcules
Total (without water)58,0221
Polymers58,0221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.539, 92.539, 127.911
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein SQHop_cyclase_C domain-containing protein


Mass: 58021.641 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kitasatospora sp. CB02891 (bacteria) / Gene: CG736_03410 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2M9LDX2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.99 Å3/Da / Density % sol: 58.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.01 M Zin sulfate heptahydrate, 0.1 M MES monohydrate, ph 6.5, 25% polyethylene glycol monomethyl ether 550

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 0.9732 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9732 Å / Relative weight: 1
ReflectionResolution: 2.57→30 Å / Num. obs: 38716 / % possible obs: 99.3 % / Redundancy: 4.7 % / CC1/2: 0.84 / Rmerge(I) obs: 0.12 / Net I/σ(I): 15.66
Reflection shellResolution: 2.57→2.67 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.603 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 4301 / CC1/2: 0.711 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
SCALAdata scaling
PDB_EXTRACT3.27data extraction
MOLREPphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BP8

5bp8


Resolution: 2.57→27.39 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.875 / SU B: 14.165 / SU ML: 0.308 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.731 / ESU R Free: 0.344 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2879 2048 5.3 %RANDOM
Rwork0.2529 ---
obs0.2548 36668 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 123.7 Å2 / Biso mean: 53.781 Å2 / Biso min: 27.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.02 Å2-0 Å2
2---0.04 Å2-0 Å2
3---0.13 Å2
Refinement stepCycle: final / Resolution: 2.57→27.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7443 0 0 160 7603
Biso mean---50.16 -
Num. residues----967
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0137639
X-RAY DIFFRACTIONr_bond_other_d0.0020.0177032
X-RAY DIFFRACTIONr_angle_refined_deg1.3241.64510413
X-RAY DIFFRACTIONr_angle_other_deg1.2781.57416235
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0685958
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.5321.266403
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.523151155
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7811562
X-RAY DIFFRACTIONr_chiral_restr0.0610.2972
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028687
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021733
LS refinement shellResolution: 2.57→2.636 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 159 -
Rwork0.296 2708 -
all-2867 -
obs--99.97 %

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