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- PDB-7v0d: Crystal structure of halogenase CtcP from Kitasatospora aureofaciens -

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Basic information

Entry
Database: PDB / ID: 7v0d
TitleCrystal structure of halogenase CtcP from Kitasatospora aureofaciens
ComponentsTetracycline 7-halogenase
KeywordsOXIDOREDUCTASE / Chlortetracycline / Biosynthesis / Chlorinase / FAD Binding / ANTIBIOTIC
Function / homology
Function and homology information


tetracycline 7-halogenase / antibiotic biosynthetic process / FAD binding / oxidoreductase activity
Similarity search - Function
: / FAD-binding domain / FAD binding domain / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Tetracycline 7-halogenase
Similarity search - Component
Biological speciesKitasatospora aureofaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHou, C. / Tsodikov, O.V.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: To Be Published
Title: Crystal structures and complex formation of halogenase CtcP and FAD reductase CtcQ from the chlortetracycline biosynthetic pathway
Authors: Hou, C. / Garneau-Tsodikova, S. / Tsodikov, O.V.
History
DepositionMay 10, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: 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: Tetracycline 7-halogenase
B: Tetracycline 7-halogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,01219
Polymers126,1552
Non-polymers1,85717
Water5,819323
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)98.591, 106.035, 178.594
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Tetracycline 7-halogenase / FADH2-dependent halogenase


Mass: 63077.574 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The N-terminal GPH is a cloning artifact left after N-terminal tag cleavage
Source: (gene. exp.) Kitasatospora aureofaciens (bacteria) / Gene: ctcP, cts4, B6264_18525, HS99_0013305 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1E7MYN1, tetracycline 7-halogenase

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Non-polymers , 7 types, 340 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.7 Å3/Da / Density % sol: 66.76 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1.6M ammonium sulfate, Hepes pH 7.0, 2% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 58486 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 8.6 % / CC1/2: 0.989 / Rmerge(I) obs: 0.147 / Net I/σ(I): 13
Reflection shellResolution: 2.6→2.64 Å / Num. unique obs: 2868 / CC1/2: 0.895

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BZQ

6bzq


Resolution: 2.6→35 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.929 / SU B: 9.029 / SU ML: 0.182 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.332 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2192 2815 4.8 %RANDOM
Rwork0.1865 ---
obs0.188 55309 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 133.14 Å2 / Biso mean: 42.454 Å2 / Biso min: 11.1 Å2
Baniso -1Baniso -2Baniso -3
1-4.3 Å20 Å20 Å2
2---0.62 Å20 Å2
3----3.68 Å2
Refinement stepCycle: final / Resolution: 2.6→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8476 0 106 323 8905
Biso mean--64.65 39.61 -
Num. residues----1063
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0138798
X-RAY DIFFRACTIONr_bond_other_d0.0020.0177819
X-RAY DIFFRACTIONr_angle_refined_deg1.1951.64111938
X-RAY DIFFRACTIONr_angle_other_deg1.1181.57818055
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.28851061
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.13420.775542
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.411151357
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6211587
X-RAY DIFFRACTIONr_chiral_restr0.0420.21094
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.029989
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022064
LS refinement shellResolution: 2.6→2.667 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 222 -
Rwork0.275 4009 -
all-4231 -
obs--99.91 %

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