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- PDB-8b7s: Crystal structure of the Chloramphenicol-inactivating oxidoreduct... -

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Basic information

Entry
Database: PDB / ID: 8b7s
TitleCrystal structure of the Chloramphenicol-inactivating oxidoreductase from Novosphingobium sp
ComponentsChloramphenicol-inactivating oxidoreductase
KeywordsFLAVOPROTEIN / CAP-oHase / Chloramphenicol / Oxidoreductase / Flavin / FAD / CAP / anitmicrobial resistance
Function / homologyFLAVIN-ADENINE DINUCLEOTIDE
Function and homology information
Biological speciesNovosphingobium sp. B 225 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsZhang, L. / Toplak, M. / Saleem-Batcha, R. / Hoeing, L. / Jakob, R.P. / Jehmlich, N. / von Bergen, M. / Maier, T. / Teufel, R.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)TE 931/3-1 Germany
German Research Foundation (DFG)TE 931/4-1 Germany
CitationJournal: Chembiochem / Year: 2023
Title: Bacterial Dehydrogenases Facilitate Oxidative Inactivation and Bioremediation of Chloramphenicol.
Authors: Zhang, L. / Toplak, M. / Saleem-Batcha, R. / Hoing, L. / Jakob, R. / Jehmlich, N. / von Bergen, M. / Maier, T. / Teufel, R.
History
DepositionOct 3, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 30, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Dec 7, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Dec 14, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.5Feb 1, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year
Revision 1.6May 1, 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: Chloramphenicol-inactivating oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5052
Polymers58,7191
Non-polymers7861
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-7 kcal/mol
Surface area18390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.623, 43.806, 164.698
Angle α, β, γ (deg.)90.000, 91.060, 90.000
Int Tables number5
Space group name H-MI121

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Components

#1: Protein Chloramphenicol-inactivating oxidoreductase


Mass: 58719.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Novosphingobium sp. B 225 (bacteria) / Plasmid: pET11-M11-His-TEV / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.29 Å3/Da / Density % sol: 46.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Morpheus-D03: 10% w/v PEG 4000, 20% v/v glycerol 0.02 M of each alcohol (1,6-hexanediol, M 1-butanol, (RS)-1,2-propanediol, 2-propanol, 1,4-butanediol, 1,3-propanediol), 0.1 M MES/imidazole pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00004 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 2.1→44.609 Å / Num. obs: 31156 / % possible obs: 98.7 % / Redundancy: 6.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.055 / Net I/σ(I): 9.8
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 7.2 % / Rmerge(I) obs: 1.702 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2528 / CC1/2: 0.54 / Rpim(I) all: 0.732 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 2.1→44.609 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.232 1636 5.26 %
Rwork0.2071 29494 -
obs0.2085 31130 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 201.74 Å2 / Biso mean: 68.6075 Å2 / Biso min: 6.41 Å2
Refinement stepCycle: final / Resolution: 2.1→44.609 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3482 0 84 115 3681
Biso mean--38.49 71.13 -
Num. residues----458
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1-2.16180.34081420.3252241599
2.1618-2.23160.35071300.3149242899
2.2316-2.31130.28511330.2813247699
2.3113-2.40390.31261150.2392244298
2.4039-2.51330.24921400.2198239099
2.5133-2.64580.25241420.21852470100
2.6458-2.81150.26351460.22022457100
2.8115-3.02850.26091280.2256248399
3.0285-3.33320.24091570.2101243398
3.3332-3.81530.2251240.1957243597
3.8153-4.8060.19521340.162252499
4.806-44.6090.19531450.1993254198
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.2831-0.8085-0.34681.82320.04742.466-0.0340.0003-0.23150.1664-0.10530.0810.0883-0.1490.12420.3337-0.0682-0.01660.24130.00560.29689.3003-2.289819.6526
22.3297-0.1773-0.88271.54041.31992.2659-0.0177-0.0533-0.2666-0.128-0.32360.40390.2102-0.97770.26910.5425-0.0920.0170.8358-0.11680.6136-18.9418-3.87219.8765
31.6005-0.37170.00731.73660.122.1784-0.08110.0172-0.04160.2702-0.0355-0.24280.01310.0820.12530.3909-0.0496-0.05930.25120.04360.310414.25540.201423.798
43.39942.1155-2.19515.3954-3.06514.8877-0.44930.1647-0.3716-0.49790.302-0.24330.6837-0.45160.04690.4847-0.0550.06370.68-0.08220.5474-16.138-0.370220.2556
52.8348-0.21910.38111.31230.16321.5955-0.1759-0.25770.20770.2178-0.04150.218-0.198-0.60440.19280.4070.02420.01950.4941-0.05520.3643-4.43147.4124.6991
64.5306-0.6838-0.42783.11210.61064.528-0.09960.7713-0.1836-0.2637-0.1225-0.2527-0.23090.02940.14650.3259-0.0097-0.01550.3140.04020.282116.3178-0.4749.5918
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 132 )A2 - 132
2X-RAY DIFFRACTION2chain 'A' and (resid 133 through 181 )A133 - 181
3X-RAY DIFFRACTION3chain 'A' and (resid 182 through 304 )A182 - 304
4X-RAY DIFFRACTION4chain 'A' and (resid 305 through 386 )A305 - 386
5X-RAY DIFFRACTION5chain 'A' and (resid 387 through 513 )A387 - 513
6X-RAY DIFFRACTION6chain 'A' and (resid 514 through 537 )A514 - 537

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