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- PDB-8yjo: Structure of E. coli glycyl radical enzyme PflD with bound malonate -

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Basic information

Entry
Database: PDB / ID: 8yjo
TitleStructure of E. coli glycyl radical enzyme PflD with bound malonate
ComponentsProbable dehydratase PflD
KeywordsLYASE / Glycyl radical enzyme
Function / homology
Function and homology information


Lyases; Carbon-oxygen lyases; Hydro-lyases / lyase activity / cytosol
Similarity search - Function
Glycyl radical enzyme, PFL2/glycerol dehydratase family / : / Pyruvate formate lyase domain / Pyruvate formate lyase-like / Pyruvate formate-lyase domain profile. / Glycine radical / Formate C-acetyltransferase glycine radical, conserved site / Glycine radical domain signature. / Glycine radical domain / Glycine radical domain profile.
Similarity search - Domain/homology
MALONATE ION / Probable dehydratase PflD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsXue, B. / Wei, Y. / Robinson, R.C. / Yew, W.S. / Zhang, Y.
Funding support Singapore, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Singapore) Singapore
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
DepositionMar 2, 2024Deposition site: PDBJ / Processing site: PDBJ
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

Downloads & links

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Assembly

Deposited unit
A: Probable dehydratase PflD
B: Probable dehydratase PflD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,7014
Polymers175,4972
Non-polymers2042
Water18,9521052
1
A: Probable dehydratase PflD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,8502
Polymers87,7481
Non-polymers1021
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable dehydratase PflD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,8502
Polymers87,7481
Non-polymers1021
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.296, 127.662, 89.751
Angle α, β, γ (deg.)90.00, 107.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Probable dehydratase PflD


Mass: 87748.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: pflD, yijL, b3951, JW3923 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P32674, Lyases; Carbon-oxygen lyases; Hydro-lyases
#2: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H2O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1052 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.56 Å3/Da / Density % sol: 51.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1M TRIS pH 8.5, 1M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→30.02 Å / Num. obs: 153436 / % possible obs: 96.8 % / Redundancy: 3.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.061 / Rrim(I) all: 0.116 / Χ2: 0.49 / Net I/σ(I): 8.3 / Num. measured all: 541161
Reflection shellResolution: 1.8→1.83 Å / % possible obs: 74.1 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.744 / Num. measured all: 13620 / Num. unique obs: 5811 / CC1/2: 0.472 / Rpim(I) all: 0.633 / Rrim(I) all: 0.984 / Χ2: 0.46 / Net I/σ(I) obs: 0.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→30.02 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2023 7619 4.97 %
Rwork0.1702 --
obs0.1718 153383 96.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→30.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12082 0 14 1052 13148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712332
X-RAY DIFFRACTIONf_angle_d0.87616702
X-RAY DIFFRACTIONf_dihedral_angle_d5.8671678
X-RAY DIFFRACTIONf_chiral_restr0.0521862
X-RAY DIFFRACTIONf_plane_restr0.0092194
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.35091770.30373628X-RAY DIFFRACTION72
1.82-1.850.32242010.29213914X-RAY DIFFRACTION79
1.85-1.870.29212170.27714290X-RAY DIFFRACTION84
1.87-1.890.30722310.2644352X-RAY DIFFRACTION88
1.89-1.920.29081910.24194626X-RAY DIFFRACTION91
1.92-1.940.26032720.22844691X-RAY DIFFRACTION95
1.94-1.970.24152640.21244876X-RAY DIFFRACTION98
1.97-20.23572580.19945026X-RAY DIFFRACTION100
2-2.030.24642650.1884998X-RAY DIFFRACTION100
2.03-2.060.21522920.18645005X-RAY DIFFRACTION100
2.06-2.10.2152620.18374984X-RAY DIFFRACTION100
2.1-2.140.2352400.17845023X-RAY DIFFRACTION100
2.14-2.180.20892380.1775051X-RAY DIFFRACTION100
2.18-2.220.21012970.16774962X-RAY DIFFRACTION100
2.22-2.270.22882480.16575000X-RAY DIFFRACTION100
2.27-2.320.20472700.16395017X-RAY DIFFRACTION100
2.32-2.380.19832440.1625010X-RAY DIFFRACTION100
2.38-2.450.20462720.16635033X-RAY DIFFRACTION100
2.45-2.520.22212750.17225003X-RAY DIFFRACTION100
2.52-2.60.22152720.18575021X-RAY DIFFRACTION100
2.6-2.690.21922720.18324984X-RAY DIFFRACTION100
2.69-2.80.22162520.18915035X-RAY DIFFRACTION100
2.8-2.930.22742460.18945015X-RAY DIFFRACTION100
2.93-3.080.20682710.18255025X-RAY DIFFRACTION100
3.08-3.280.19952360.16635069X-RAY DIFFRACTION100
3.28-3.530.1832630.14265008X-RAY DIFFRACTION100
3.53-3.880.14862700.13335036X-RAY DIFFRACTION100
3.88-4.440.14752490.1195043X-RAY DIFFRACTION100
4.44-5.590.1472870.13165024X-RAY DIFFRACTION100
5.59-30.020.15792870.14375015X-RAY DIFFRACTION98

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