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- PDB-8ki5: PhmA, a type I diterpene synthase without NST/DTE motif -

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Basic information

Entry
Database: PDB / ID: 8ki5
TitlePhmA, a type I diterpene synthase without NST/DTE motif
ComponentsPhmA
KeywordsBIOSYNTHETIC PROTEIN / diterpene synthase
Function / homology(2Z,6Z)-3,7,11-trimethyldodeca-2,6,10-trien-1-ol
Function and homology information
Biological speciesPhoma (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 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 22, 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:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PhmA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7072
Polymers37,4841
Non-polymers2221
Water2,036113
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.900, 105.900, 54.380
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-613-

HOH

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Components

#1: Protein 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-FOH / (2Z,6Z)-3,7,11-trimethyldodeca-2,6,10-trien-1-ol / cis,cis-Farnesol


Mass: 222.366 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C15H26O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.35 Å3/Da / Density % sol: 47.62 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion / pH: 5.6
Details: 1.0 M Lithium sulfate, 0.1 M Sodium citrate pH 5.6, 0.5 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97919 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 17, 2020
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 2.01→54.38 Å / Num. obs: 23328 / % possible obs: 99.9 % / Redundancy: 20 % / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Net I/σ(I): 22.7
Reflection shellResolution: 2.01→2.06 Å / Num. unique obs: 1705 / CC1/2: 0.808
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→29.23 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 0.05 / Phase error: 24.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2233 1900 8.54 %
Rwork0.1822 --
obs0.1858 22247 95.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.01→29.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2264 0 16 113 2393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142324
X-RAY DIFFRACTIONf_angle_d1.2243137
X-RAY DIFFRACTIONf_dihedral_angle_d21.133868
X-RAY DIFFRACTIONf_chiral_restr0.06343
X-RAY DIFFRACTIONf_plane_restr0.014409
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.060.30771120.23491282X-RAY DIFFRACTION85
2.06-2.120.27631280.22141333X-RAY DIFFRACTION88
2.12-2.180.29651320.22281379X-RAY DIFFRACTION91
2.18-2.250.22861320.19681415X-RAY DIFFRACTION94
2.25-2.330.26331330.19041407X-RAY DIFFRACTION93
2.33-2.420.21811360.19221457X-RAY DIFFRACTION96
2.42-2.530.26861380.19241441X-RAY DIFFRACTION95
2.53-2.670.23871360.20031481X-RAY DIFFRACTION97
2.67-2.830.29981340.19911489X-RAY DIFFRACTION98
2.83-3.050.2711460.21611501X-RAY DIFFRACTION99
3.05-3.360.26521420.21091528X-RAY DIFFRACTION99
3.36-3.840.19771410.17481538X-RAY DIFFRACTION100
3.84-4.840.17261450.15611537X-RAY DIFFRACTION100
4.84-29.230.20511450.16311559X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -36.1527 Å / Origin y: -10.5867 Å / Origin z: -9.215 Å
111213212223313233
T0.3141 Å20.0125 Å20.0354 Å2-0.3137 Å20.0537 Å2--0.3114 Å2
L1.9128 °2-0.9053 °20.8723 °2-2.6363 °2-1.01 °2--1.4858 °2
S0.0417 Å °-0.0301 Å °-0.0232 Å °-0.0427 Å °-0.1416 Å °-0.2224 Å °0.0461 Å °0.1787 Å °0.1007 Å °
Refinement TLS groupSelection details: all

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