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- PDB-7yhe: Crystal structure of the triple mutant CmnC-L136Q,S138G,D249Y in ... -

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Basic information

Entry
Database: PDB / ID: 7yhe
TitleCrystal structure of the triple mutant CmnC-L136Q,S138G,D249Y in complex with alpha-KG
ComponentsCmnC
KeywordsOXIDOREDUCTASE / hydroxylase / oxygenase
Function / homology
Function and homology information


oxidoreductase activity / iron ion binding
Similarity search - Function
Arginine beta-hydroxylase, Fe2/alpha-ketoglutarate-dependent / : / Clavaminate synthase-like / TauD/TfdA-like domain / Taurine catabolism dioxygenase TauD, TfdA family / Taurine dioxygenase TauD-like superfamily
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / : / TRIETHYLENE GLYCOL / CmnC
Similarity search - Component
Biological speciesSaccharothrix mutabilis subsp. capreolus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsHuang, S.J. / Hsiao, Y.H. / Lin, E.C. / Hsiao, P.Y. / Chang, C.Y.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)110-2113-M-A49 -026 -MY3 Taiwan
CitationJournal: Front Chem / Year: 2022
Title: Crystal structure of the alpha-ketoglutarate-dependent non-heme iron oxygenase CmnC in capreomycin biosynthesis and its engineering to catalyze hydroxylation of the substrate enantiomer.
Authors: Hsiao, Y.H. / Huang, S.J. / Lin, E.C. / Hsiao, P.Y. / Toh, S.I. / Chen, I.H. / Xu, Z. / Lin, Y.P. / Liu, H.J. / Chang, C.Y.
History
DepositionJul 13, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
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.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CmnC
B: CmnC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,7396
Polymers78,2412
Non-polymers4984
Water9,224512
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-0 kcal/mol
Surface area25510 Å2
Unit cell
Length a, b, c (Å)93.115, 127.191, 138.759
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11B-601-

HOH

21B-712-

HOH

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Components

#1: Protein CmnC


Mass: 39120.562 Da / Num. of mol.: 2 / Mutation: 136Q,S138G,D249Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharothrix mutabilis subsp. capreolus (bacteria)
Gene: cmnC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A6YEH4
#2: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 512 / 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: 2.63 Å3/Da / Density % sol: 53.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20 mM ammonium acetate, 24% v/v polyethylene glycol 400, 0.1 M sodium citrate tribasic dihydrate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jun 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.67→30 Å / Num. obs: 95108 / % possible obs: 99.9 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 24.05
Reflection shellResolution: 1.67→1.73 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 2.02 / Num. unique obs: 9456 / CC1/2: 0.757 / % possible all: 100

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Processing

Software
NameVersionClassification
SCALAdata scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WBO

2wbo


Resolution: 1.67→27.67 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.674 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1936 4533 5 %RANDOM
Rwork0.178 ---
obs0.1788 85445 94.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 75.59 Å2 / Biso mean: 16.668 Å2 / Biso min: 5.64 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å2-0 Å2
2---0.15 Å20 Å2
3---0.31 Å2
Refinement stepCycle: final / Resolution: 1.67→27.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5228 0 31 512 5771
Biso mean--28.91 23.98 -
Num. residues----678
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0135362
X-RAY DIFFRACTIONr_bond_other_d0.0020.0175013
X-RAY DIFFRACTIONr_angle_refined_deg1.2791.6417291
X-RAY DIFFRACTIONr_angle_other_deg1.3241.58311445
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9285675
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.10619.738343
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.43415807
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5371570
X-RAY DIFFRACTIONr_chiral_restr0.060.2669
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026229
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021327
LS refinement shellResolution: 1.67→1.713 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 264 -
Rwork0.22 4689 -
all-4953 -
obs--71.2 %

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