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- PDB-7vua: Anaerobic hydroxyproline degradation involving C-N cleavage by a ... -

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Basic information

Entry
Database: PDB / ID: 7vua
TitleAnaerobic hydroxyproline degradation involving C-N cleavage by a glycyl radical enzyme
ComponentsHplG
KeywordsLYASE / C-N-lyase
Function / homologyPyruvate formate lyase domain / Pyruvate formate lyase-like / Pyruvate formate-lyase domain profile. / Glycine radical / Glycine radical domain / Glycine radical domain profile. / catalytic activity / (4S)-4-hydroxy-D-proline / Uncharacterized protein
Function and homology information
Biological speciesClostridiales bacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.695 Å
AuthorsDuan, Y. / Lu, Q. / Yuchi, Z. / Zhang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31870049 China
CitationJournal: J.Am.Chem.Soc. / Year: 2022
Title: Anaerobic Hydroxyproline Degradation Involving C-N Cleavage by a Glycyl Radical Enzyme.
Authors: Duan, Y. / Wei, Y. / Xing, M. / Liu, J. / Jiang, L. / Lu, Q. / Liu, X. / Liu, Y. / Ang, E.L. / Liao, R.Z. / Yuchi, Z. / Zhao, H. / Zhang, Y.
History
DepositionNov 1, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2022Group: Database references / Category: citation / citation_author
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
Revision 1.2Apr 3, 2024Group: 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: HplG
B: HplG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,2064
Polymers177,9432
Non-polymers2622
Water6,341352
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-27 kcal/mol
Surface area48820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.841, 218.212, 168.174
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein HplG


Mass: 88971.680 Da / Num. of mol.: 2 / Mutation: E106A/E107A/E108A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridiales bacterium (bacteria) / Gene: DBY07_03870 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A316Q2B4
#2: Chemical ChemComp-UY7 / (4S)-4-hydroxy-D-proline


Type: D-peptide linking / Mass: 131.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 352 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.03 Å3/Da / Density % sol: 59.42 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.1M HEPES pH 7.5, 10% (w/v) PEG 8000, 8% (v/v) Ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.695→50 Å / Num. obs: 59889 / % possible obs: 100 % / Redundancy: 13.3 % / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.04 / Rrim(I) all: 0.147 / Χ2: 0.677 / Net I/σ(I): 3.6
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
2.7-2.7513.50.93929310.8310.2630.9750.429
2.75-2.813.60.84529270.8770.2360.8770.436
2.8-2.8513.60.71229870.9150.1990.740.455
2.85-2.9113.50.62529680.9290.1760.650.454
2.91-2.9713.30.53229740.9340.1510.5540.469
2.97-3.0412.70.4629630.9530.1340.480.487
3.04-3.1213.10.39229790.9690.1120.4080.494
3.12-3.213.90.32929480.9740.0910.3420.519
3.2-3.313.90.27929810.9820.0770.290.54
3.3-3.413.80.23129610.9880.0640.240.586
3.4-3.5213.50.19330060.9910.0540.20.658
3.52-3.66130.16530050.9920.0470.1720.715
3.66-3.8312.80.13829480.9930.040.1440.841
3.83-4.0313.60.12129910.9950.0340.1260.918
4.03-4.2913.80.1130110.9960.0310.1140.987
4.29-4.6213.60.09829990.9960.0270.1021.067
4.62-5.0812.70.08930180.9970.0260.0931.056
5.08-5.8113.70.08630430.9970.0240.090.865
5.81-7.3212.90.07530670.9980.0220.0780.743
7.32-5012.30.05131820.9990.0150.0530.817

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Processing

Software
NameVersionClassification
PHENIX1.14_3247refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Phyre2 prediction struction

Resolution: 2.695→32.142 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 25.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2432 1931 3.35 %
Rwork0.1737 55631 -
obs0.176 57562 95.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.66 Å2 / Biso mean: 46.5257 Å2 / Biso min: 16.16 Å2
Refinement stepCycle: final / Resolution: 2.695→32.142 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12186 0 34 352 12572
Biso mean--52.63 39.38 -
Num. residues----1570
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.695-2.76230.36531290.2579344684
2.7623-2.83690.31191180.2267364189
2.8369-2.92030.2841320.2063375892
2.9203-3.01450.28741370.2035384793
3.0145-3.12220.27641260.2012390795
3.1222-3.24710.28691410.1875397297
3.2471-3.39470.25551350.1829400997
3.3947-3.57350.25041420.177407099
3.5735-3.7970.25541490.1636409099
3.797-4.08970.22411320.1559411299
4.0897-4.50020.20931470.14484134100
4.5002-5.14910.21011470.14564179100
5.1491-6.47860.24051430.1884201100
6.4786-32.1420.21641530.1684426598

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