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- PDB-7v0b: Crystal structure of halogenase CtcP from Kitasatospora aureofaci... -

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Basic information

Entry
Database: PDB / ID: 7v0b
TitleCrystal structure of halogenase CtcP from Kitasatospora aureofaciens in complex with FAD
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
FLAVIN-ADENINE DINUCLEOTIDE / Tetracycline 7-halogenase
Similarity search - Component
Biological speciesKitasatospora aureofaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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
C: Tetracycline 7-halogenase
D: Tetracycline 7-halogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)256,37018
Polymers252,3104
Non-polymers4,06014
Water16,970942
1
A: Tetracycline 7-halogenase
B: Tetracycline 7-halogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,2209
Polymers126,1552
Non-polymers2,0647
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Tetracycline 7-halogenase
D: Tetracycline 7-halogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,1519
Polymers126,1552
Non-polymers1,9957
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.764, 103.576, 179.216
Angle α, β, γ (deg.)90.000, 95.400, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 63077.574 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: The N-terminal GPH sequence is a cloning artifact, left from the N-terminal tag after 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 , 6 types, 956 molecules

#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 942 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.3 Å3/Da / Density % sol: 46.49 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 26% PEG 4000, 100 mM Hepes pH 7.5, 200 mM lithium sulfate

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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: Oct 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 121382 / % possible obs: 96.9 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / CC1/2: 0.982 / Rmerge(I) obs: 0.137 / Net I/σ(I): 15
Reflection shellResolution: 2.15→2.19 Å / Rmerge(I) obs: 0.796 / Num. unique obs: 6180 / CC1/2: 0.685

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BZQ

6bzq


Resolution: 2.15→35 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.926 / SU B: 6.489 / SU ML: 0.161 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.275 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2327 6167 5.1 %RANDOM
Rwork0.1879 ---
obs0.1902 114137 96.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 77.73 Å2 / Biso mean: 29.503 Å2 / Biso min: 5.1 Å2
Baniso -1Baniso -2Baniso -3
1-3.14 Å20 Å2-0.76 Å2
2---1.3 Å20 Å2
3----1.66 Å2
Refinement stepCycle: final / Resolution: 2.15→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16973 0 263 942 18178
Biso mean--51.12 35.53 -
Num. residues----2129
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01317712
X-RAY DIFFRACTIONr_bond_other_d0.0010.01715923
X-RAY DIFFRACTIONr_angle_refined_deg1.2341.64124102
X-RAY DIFFRACTIONr_angle_other_deg1.1591.57636547
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.54352125
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.33920.7471085
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.908152719
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.21315175
X-RAY DIFFRACTIONr_chiral_restr0.050.22221
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0220300
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024434
LS refinement shellResolution: 2.15→2.206 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 451 -
Rwork0.254 8585 -
all-9036 -
obs--99.09 %

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