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- PDB-8id0: Crystal structure of PflD bound to 1,5-anhydromannitol-6-phosphat... -

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Basic information

Entry
Database: PDB / ID: 8id0
TitleCrystal structure of PflD bound to 1,5-anhydromannitol-6-phosphate in Streptococcus dysgalactiae subsp. equisimilis
Componentsformate C-acetyltransferase
KeywordsLYASE / glycyl radical enzyme / PflD / 1 / 5-anhydromannitol-6-phosphate
Function / homology:
Function and homology information
Biological speciesStreptococcus dysgalactiae subsp. equisimilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsMa, K.L. / Zhang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: J.Am.Chem.Soc. / Year: 2024
Title: A Widespread Radical-Mediated Glycolysis Pathway.
Authors: Ma, K. / Xue, B. / Chu, R. / Zheng, Y. / Sharma, S. / Jiang, L. / Hu, M. / Xie, Y. / Hu, Y. / Tao, T. / Zhou, Y. / Liu, D. / Li, Z. / Yang, Q. / Chen, Y. / Wu, S. / Tong, Y. / Robinson, R.C. ...Authors: Ma, K. / Xue, B. / Chu, R. / Zheng, Y. / Sharma, S. / Jiang, L. / Hu, M. / Xie, Y. / Hu, Y. / Tao, T. / Zhou, Y. / Liu, D. / Li, Z. / Yang, Q. / Chen, Y. / Wu, S. / Tong, Y. / Robinson, R.C. / Yew, W.S. / Jin, X. / Liu, Y. / Zhao, H. / Ang, E.L. / Wei, Y. / Zhang, Y.
History
DepositionFeb 11, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: formate C-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,4152
Polymers88,1711
Non-polymers2441
Water10,160564
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)183.912, 183.912, 60.025
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

#1: Protein formate C-acetyltransferase


Mass: 88171.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus dysgalactiae subsp. equisimilis (bacteria)
Production host: Escherichia coli (E. coli) / References: 4-hydroxyphenylacetate decarboxylase
#2: Chemical ChemComp-7P6 / [(2R,3S,4R,5R)-3,4,5-tris(oxidanyl)oxan-2-yl]methyl dihydrogen phosphate


Mass: 244.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 564 / 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: 3.32 Å3/Da / Density % sol: 62.99 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 1.2 M sodium citrate, 0.1 M sodium HEPES, pH 8.0, 10 mM 1,5-anhydromannitol-6-phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.34→159.27 Å / Num. obs: 49308 / % possible obs: 100 % / Redundancy: 9.6 % / CC1/2: 0.983 / Rmerge(I) obs: 0.199 / Rpim(I) all: 0.105 / Rrim(I) all: 0.317 / Χ2: 0.8 / Net I/σ(I): 12.3
Reflection shellResolution: 2.34→2.4 Å / Redundancy: 8 % / Rmerge(I) obs: 1.792 / Num. unique obs: 3629 / CC1/2: 0.446 / Rpim(I) all: 0.82 / Χ2: 0.82

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Processing

Software
NameVersionClassification
PHENIX1.14refinement
DIALSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.34→60.199 Å / SU ML: 0.19 / Cross valid method: NONE / σ(F): 0 / Phase error: 18.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1929 1960 4.02 %
Rwork0.1569 --
obs0.1583 48714 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.34→60.199 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6103 0 15 564 6682
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076254
X-RAY DIFFRACTIONf_angle_d0.8438488
X-RAY DIFFRACTIONf_dihedral_angle_d7.915178
X-RAY DIFFRACTIONf_chiral_restr0.051949
X-RAY DIFFRACTIONf_plane_restr0.0051104
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3401-2.39860.24461370.19013243X-RAY DIFFRACTION97
2.3986-2.46350.2221290.19123213X-RAY DIFFRACTION97
2.4635-2.5360.22611390.18683270X-RAY DIFFRACTION98
2.536-2.61780.23061370.1893323X-RAY DIFFRACTION98
2.6178-2.71140.23381420.17993317X-RAY DIFFRACTION99
2.7114-2.81990.2441310.18443283X-RAY DIFFRACTION98
2.8199-2.94830.21441400.18413335X-RAY DIFFRACTION99
2.9483-3.10370.2351450.17483339X-RAY DIFFRACTION99
3.1037-3.29820.20821420.16533361X-RAY DIFFRACTION100
3.2982-3.55280.1731390.15723385X-RAY DIFFRACTION100
3.5528-3.91030.17671410.13863370X-RAY DIFFRACTION100
3.9103-4.47590.14751440.12163394X-RAY DIFFRACTION100
4.4759-5.63850.16791440.1263417X-RAY DIFFRACTION100
5.6385-60.1990.1661500.1483504X-RAY DIFFRACTION100

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