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- PDB-8id1: Crystal structure of N-Methyl-cis-4-hydroxy-L-proline dehydratase... -

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Basic information

Entry
Database: PDB / ID: 8id1
TitleCrystal structure of N-Methyl-cis-4-hydroxy-L-proline dehydratase in Intestinibacter bartlettii
ComponentsFormate C-acetyltransferase
KeywordsLYASE / Glycyl Radical Enzymes / dehydratase
Function / homology:
Function and homology information
Biological speciesIntestinibacter bartlettii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.115 Å
AuthorsJiang, L. / Zhang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Acs Catalysis / Year: 2024
Title: Glycyl Radical Enzymes Catalyzing the Dehydration of Two Isomers of N-Methyl-4-hydroxyproline
Authors: Jiang, L. / Yang, Y. / Huang, L. / Zhou, Y. / An, J. / Zheng, Y. / Chen, Y. / Liu, Y. / Huang, J. / Ang, E.L. / Zhao, S. / Zhao, H. / Liao, R. / Wei, Y. / Zhang, Y.
History
DepositionFeb 11, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 9, 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_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _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: Formate C-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,6112
Polymers89,4661
Non-polymers1451
Water00
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)142.747, 142.747, 101.032
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Formate C-acetyltransferase


Mass: 89466.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The protein was from Intestinibacter bartlettii (GenBank assess number: MCB5397844.1)
Source: (gene. exp.) Intestinibacter bartlettii (bacteria) / Gene: C7955_105265 / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-6IW / (2S,4S)-1-methyl-4-oxidanyl-pyrrolidine-2-carboxylic acid


Mass: 145.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11NO3 / Feature type: SUBJECT OF INVESTIGATION
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: 2.89 Å3/Da / Density % sol: 57.44 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium chloride, 0.1 M Bis-Tris, pH 6.5, 1.5 M ammonium sulfate, 50 mM cis-N-Methylhydroxy-L-proline

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Dec 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.11→82.47 Å / Num. obs: 19290 / % possible obs: 100 % / Redundancy: 16.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.237 / Rpim(I) all: 0.059 / Rrim(I) all: 0.245 / Χ2: 1.01 / Net I/σ(I): 13.3 / Num. measured all: 315129
Reflection shellResolution: 3.11→3.28 Å / % possible obs: 100 % / Redundancy: 16.1 % / Rmerge(I) obs: 1.508 / Num. measured all: 44587 / Num. unique obs: 2763 / CC1/2: 0.833 / Rpim(I) all: 0.381 / Rrim(I) all: 1.556 / Χ2: 0.89 / Net I/σ(I) obs: 2.6

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Processing

Software
NameVersionClassification
Aimlessdata scaling
XDSdata reduction
PHENIX1.14refinement
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.115→50.516 Å / SU ML: 0.49 / Cross valid method: NONE / σ(F): 0 / Phase error: 32.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3094 1795 9.94 %
Rwork0.2111 --
obs0.2209 18056 93.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.115→50.516 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6175 0 10 0 6185
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016306
X-RAY DIFFRACTIONf_angle_d1.3618511
X-RAY DIFFRACTIONf_dihedral_angle_d4.9143812
X-RAY DIFFRACTIONf_chiral_restr0.065931
X-RAY DIFFRACTIONf_plane_restr0.0081102
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.115-3.19870.40611290.31621175X-RAY DIFFRACTION90
3.1987-3.29280.40631270.29561190X-RAY DIFFRACTION91
3.2928-3.39910.42291340.28691162X-RAY DIFFRACTION90
3.3991-3.52050.37261340.26821196X-RAY DIFFRACTION92
3.5205-3.66140.32051300.25611219X-RAY DIFFRACTION92
3.6614-3.8280.33581340.21341195X-RAY DIFFRACTION91
3.828-4.02980.29991350.20871222X-RAY DIFFRACTION93
4.0298-4.28210.28561330.18951227X-RAY DIFFRACTION93
4.2821-4.61250.29941360.18361260X-RAY DIFFRACTION94
4.6125-5.07630.31111440.18281290X-RAY DIFFRACTION97
5.0763-5.810.2581480.20331315X-RAY DIFFRACTION98
5.81-7.31640.31821530.22111366X-RAY DIFFRACTION100
7.3164-50.50.26691580.17571444X-RAY DIFFRACTION99

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