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- PDB-7vgl: Crystal structure of CmnC -

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Basic information

Entry
Database: PDB / ID: 7vgl
TitleCrystal structure of CmnC
ComponentsCmnC
KeywordsOXIDOREDUCTASE / hydroxylase / dioxygenase
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
Biological speciesSaccharothrix mutabilis subsp. capreolus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsHsiao, Y.H. / Huang, S.J. / Lin, E.C. / Lee, Y.C. / Zheng, Y.Z. / 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
DepositionSep 17, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 21, 2022Provider: 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)78,2934
Polymers78,1752
Non-polymers1182
Water9,332518
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint4 kcal/mol
Surface area25900 Å2
Unit cell
Length a, b, c (Å)92.946, 127.400, 139.265
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-605-

HOH

21A-748-

HOH

31B-630-

HOH

41B-664-

HOH

51B-723-

HOH

61B-768-

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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 518 / 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: 2.64 Å3/Da / Density % sol: 53.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
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: 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): 24.04
Reflection shellResolution: 1.67→1.73 Å / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 2 / Num. unique obs: 9456

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Processing

Software
NameVersionClassification
SCALAdata scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WBQ

2wbq


Resolution: 1.67→25.87 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.936 / SU B: 1.904 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2099 4538 5 %RANDOM
Rwork0.1789 ---
obs0.1804 86659 95.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 80.08 Å2 / Biso mean: 17.658 Å2 / Biso min: 6.22 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å20 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.67→25.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5242 0 8 518 5768
Biso mean--23.12 25.88 -
Num. residues----680
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0135355
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175010
X-RAY DIFFRACTIONr_angle_refined_deg1.2941.6387287
X-RAY DIFFRACTIONr_angle_other_deg1.3241.58311438
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9395677
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.73519.795341
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.00515811
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4841570
X-RAY DIFFRACTIONr_chiral_restr0.060.2673
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026219
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021321
LS refinement shellResolution: 1.672→1.715 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 237 -
Rwork0.248 4337 -
all-4574 -
obs--65.79 %

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