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- PDB-8kih: PhmA, a type I diterpene synthase without NST/DTE motif -

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Basic information

Entry
Database: PDB / ID: 8kih
TitlePhmA, a type I diterpene synthase without NST/DTE motif
Componentsditerpene synthase, PhmA
KeywordsBIOSYNTHETIC PROTEIN / diterpene synthase
Function / homologyChem-FGG
Function and homology information
Biological speciesPhoma (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZhang, B. / Ge, H.M. / Zhu, A. / Zhang, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22277051, 22193071, 22107048, 22077062, 81991522, 81991524 China
Other governmentBK20220123 China
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2023
Title: Biosynthesis of Phomactin Platelet Activating Factor Antagonist Requires a Two-Enzyme Cascade.
Authors: Zhang, L. / Zhang, B. / Zhu, A. / Liu, S.H. / Wu, R. / Zhang, X. / Xu, Z. / Tan, R.X. / Ge, H.M.
History
DepositionAug 23, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 4, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: diterpene synthase, PhmA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0014
Polymers37,4841
Non-polymers5173
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-19 kcal/mol
Surface area13430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.549, 106.549, 55.360
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
Components on special symmetry positions
IDModelComponents
11A-702-

HOH

21A-724-

HOH

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Components

#1: Protein diterpene synthase, PhmA


Mass: 37484.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phoma (fungus) / Strain: sp. ATCC 74077 / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-FGG / (2Z,6E,10E)-2-fluoro-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraen-1-yl trihydrogen diphosphate / 2-fluoro-geranylgeranyl diphosphate


Mass: 468.434 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H35FO7P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 291.15 K / Method: vapor diffusion / pH: 7.5
Details: 1.6 M Ammonium sulfate, 0.1 M Sodium chloride, 0.1 M Sodium HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97851 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 24, 2022
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97851 Å / Relative weight: 1
ReflectionResolution: 1.8→35.44 Å / Num. obs: 33385 / % possible obs: 100 % / Redundancy: 19 % / CC1/2: 0.998 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.028 / Rrim(I) all: 0.124 / Χ2: 1.28 / Net I/σ(I): 17.4 / Num. measured all: 634671
Reflection shellResolution: 1.8→1.84 Å / % possible obs: 100 % / Redundancy: 17.4 % / Rmerge(I) obs: 0.797 / Num. measured all: 34274 / Num. unique obs: 1975 / CC1/2: 0.876 / Rpim(I) all: 0.196 / Rrim(I) all: 0.821 / Χ2: 0.84 / Net I/σ(I) obs: 3.8

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→34.88 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2372 1985 8.22 %
Rwork0.1925 --
obs0.1962 24153 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→34.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2310 0 32 229 2571
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012386
X-RAY DIFFRACTIONf_angle_d1.0273227
X-RAY DIFFRACTIONf_dihedral_angle_d15.754890
X-RAY DIFFRACTIONf_chiral_restr0.055353
X-RAY DIFFRACTIONf_plane_restr0.011421
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.27711420.18481609X-RAY DIFFRACTION100
2.05-2.110.22291390.17751576X-RAY DIFFRACTION100
2.11-2.170.22951400.1891582X-RAY DIFFRACTION100
2.17-2.240.27221390.19881526X-RAY DIFFRACTION97
2.24-2.320.36241360.28391443X-RAY DIFFRACTION90
2.32-2.410.22731390.19241591X-RAY DIFFRACTION100
2.41-2.520.2391400.18451574X-RAY DIFFRACTION100
2.52-2.650.24571450.20981596X-RAY DIFFRACTION100
2.65-2.820.26751460.19221592X-RAY DIFFRACTION100
2.82-3.040.26291440.19931594X-RAY DIFFRACTION100
3.04-3.340.23331430.19451610X-RAY DIFFRACTION100
3.34-3.820.22261380.17331593X-RAY DIFFRACTION100
3.83-4.820.17531480.17191626X-RAY DIFFRACTION100
4.82-34.880.23921460.19641656X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -36.418 Å / Origin y: -10.7393 Å / Origin z: -8.9853 Å
111213212223313233
T0.1506 Å20.0099 Å20.0062 Å2-0.1221 Å20.0037 Å2--0.1312 Å2
L1.0549 °2-0.6864 °20.635 °2-1.3235 °2-0.5587 °2--0.945 °2
S0.0402 Å °0.0261 Å °0.0171 Å °0.0914 Å °-0.0576 Å °-0.1081 Å °0.0258 Å °0.1658 Å °0.0085 Å °
Refinement TLS groupSelection details: all

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