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- PDB-7y5f: Crystal structure of CmnC in complex with L-homoarginine -

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Basic information

Entry
Database: PDB / ID: 7y5f
TitleCrystal structure of CmnC in complex with L-homoarginine
ComponentsCmnC
KeywordsOXIDOREDUCTASE / hydroxylase
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
: / L-HOMOARGININE / L(+)-TARTARIC ACID / CmnC
Similarity search - Component
Biological speciesSaccharothrix mutabilis subsp. capreolus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 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 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CmnC
B: CmnC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,9638
Polymers78,1752
Non-polymers7886
Water10,359575
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)93.344, 127.514, 139.034
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-560-

HOH

21A-794-

HOH

31B-603-

HOH

41B-717-

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


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-HRG / L-HOMOARGININE


Type: L-peptide linking / Mass: 188.228 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H16N4O2
#4: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 575 / 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: 55.8 %
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: BL13B1 / Wavelength: 0.9732 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 31, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9732 Å / Relative weight: 1
ReflectionResolution: 1.52→30 Å / Num. obs: 123057 / % possible obs: 98.8 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 31.9
Reflection shellResolution: 1.52→1.58 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 2.79 / Num. unique obs: 11857 / CC1/2: 0.928 / % possible all: 95.5

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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: 1.52→27.89 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.287 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2037 5570 4.9 %RANDOM
Rwork0.1799 ---
obs0.1811 107540 89.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 83.17 Å2 / Biso mean: 17.629 Å2 / Biso min: 5.9 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 1.52→27.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5242 0 48 575 5865
Biso mean--22.89 25.35 -
Num. residues----680
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0135391
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175034
X-RAY DIFFRACTIONr_angle_refined_deg1.3851.6437333
X-RAY DIFFRACTIONr_angle_other_deg1.3811.58611500
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9495677
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.4119.738343
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.5715811
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.531570
X-RAY DIFFRACTIONr_chiral_restr0.0670.2679
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026257
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021323
LS refinement shellResolution: 1.523→1.562 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 258 -
Rwork0.235 4972 -
all-5230 -
obs--56.76 %

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