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- PDB-7y5p: Crystal structure of CmnC in complex with L-arginine and alpha-KG -

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Basic information

Entry
Database: PDB / ID: 7y5p
TitleCrystal structure of CmnC in complex with L-arginine and 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 / ARGININE / : / CmnC
Similarity search - Component
Biological speciesSaccharothrix mutabilis subsp. capreolus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHsiao, Y.H. / Huang, S.J. / Lin, E.C. / Lee, Y.C. / 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
DepositionJun 17, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 5, 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)78,6986
Polymers78,1752
Non-polymers5234
Water9,062503
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)92.998, 127.292, 139.019
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
11A-562-

HOH

21B-505-

HOH

31B-636-

HOH

41B-656-

HOH

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Components

#1: Protein CmnC


Mass: 39087.531 Da / Num. of mol.: 2
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-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ARG / ARGININE / Arginine


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 503 / 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: 2.78 Å3/Da / Density % sol: 55.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2M Ammonium acetate, 0.1M Na citrate tribasic dihydrate pH 5.5, 24% v/v Polyethylene glycol 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 0.9732 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9732 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 90120 / % possible obs: 99.7 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 27.56
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.604 / Mean I/σ(I) obs: 2.42 / Num. unique obs: 8944 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
SCALAdata scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7VGL

7vgl


Resolution: 1.7→26.28 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.939 / SU B: 1.953 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2036 4384 5 %RANDOM
Rwork0.1775 ---
obs0.1788 82573 95.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.12 Å2 / Biso mean: 17.297 Å2 / Biso min: 6.52 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å2-0 Å2
2---0.04 Å20 Å2
3---0.17 Å2
Refinement stepCycle: final / Resolution: 1.7→26.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5222 0 33 503 5758
Biso mean--21.07 24.18 -
Num. residues----678
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0135356
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175015
X-RAY DIFFRACTIONr_angle_refined_deg1.2911.6417286
X-RAY DIFFRACTIONr_angle_other_deg1.321.58411450
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9355675
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.9119.679343
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.53615812
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4441571
X-RAY DIFFRACTIONr_chiral_restr0.0590.2672
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026222
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021320
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 281 -
Rwork0.236 4817 -
all-5098 -
obs--76.88 %

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