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- PDB-7xgb: Crystal structure of the ctcP from Streptomyces aureofaciens -

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Basic information

Entry
Database: PDB / ID: 7xgb
TitleCrystal structure of the ctcP from Streptomyces aureofaciens
ComponentsTetracycline 7-halogenase
KeywordsFLAVOPROTEIN / ctcP / Streptomyces aureofaciens
Function / homologytetracycline 7-halogenase / : / FAD-binding domain / FAD binding domain / antibiotic biosynthetic process / FAD binding / FAD/NAD(P)-binding domain superfamily / oxidoreductase activity / Tetracycline 7-halogenase
Function and homology information
Biological speciesKitasatospora aureofaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsYin, L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2022
Title: Crystal structure determination of the halogenase CtcP from Streptomyces aureofaciens.
Authors: Yin, L.
History
DepositionApr 4, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id ..._pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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


Theoretical massNumber of molelcules
Total (without water)254,1924
Polymers254,1924
Non-polymers00
Water5,188288
1
A: Tetracycline 7-halogenase


Theoretical massNumber of molelcules
Total (without water)63,5481
Polymers63,5481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tetracycline 7-halogenase


Theoretical massNumber of molelcules
Total (without water)63,5481
Polymers63,5481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Tetracycline 7-halogenase


Theoretical massNumber of molelcules
Total (without water)63,5481
Polymers63,5481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Tetracycline 7-halogenase


Theoretical massNumber of molelcules
Total (without water)63,5481
Polymers63,5481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.393, 121.281, 179.194
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 15 through 320 or resid 322 through 542))
21(chain B and (resid 15 through 320 or resid 322 through 542))
31(chain C and (resid 15 through 320 or resid 322 through 542))
41(chain D and (resid 15 through 320 or resid 322 through 542))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROARGARG(chain A and (resid 15 through 320 or resid 322 through 542))AA15 - 32016 - 321
12GLNGLNALAALA(chain A and (resid 15 through 320 or resid 322 through 542))AA322 - 542323 - 543
21PROPROARGARG(chain B and (resid 15 through 320 or resid 322 through 542))BB15 - 32016 - 321
22GLNGLNALAALA(chain B and (resid 15 through 320 or resid 322 through 542))BB322 - 542323 - 543
31PROPROARGARG(chain C and (resid 15 through 320 or resid 322 through 542))CC15 - 32016 - 321
32GLNGLNALAALA(chain C and (resid 15 through 320 or resid 322 through 542))CC322 - 542323 - 543
41PROPROARGARG(chain D and (resid 15 through 320 or resid 322 through 542))DD15 - 32016 - 321
42GLNGLNALAALA(chain D and (resid 15 through 320 or resid 322 through 542))DD322 - 542323 - 543

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Components

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


Mass: 63547.922 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kitasatospora aureofaciens (bacteria) / Gene: ctcP, cts4, B6264_18525, HS99_0013305 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1E7MYN1, tetracycline 7-halogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.51 Å3/Da / Density % sol: 51.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1M BIS-TRIS pH 6.0, 0.2M Magnesium sulfate heptahydrate, 20% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97923 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 70271 / % possible obs: 100 % / Redundancy: 14.8 % / Biso Wilson estimate: 37.03 Å2 / Rmerge(I) obs: 0.177 / Χ2: 1.042 / Net I/σ(I): 8.1 / Num. measured all: 1038277
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.7-2.814.90.81269090.9961100
2.8-2.9114.90.60469431.0531100
2.91-3.0414.90.44569351.0991100
3.04-3.214.90.34469611.0451100
3.2-3.414.90.24369601.0591100
3.4-3.6614.90.18270311.0381100
3.66-4.0314.90.1469961.0041100
4.03-4.6214.80.11270411.0021100
4.62-5.8114.60.12371141.0651100
5.81-50140.08273811.0561100

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Processing

Software
NameVersionClassification
PHENIX1.19refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.7→48.8 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2243 2010 2.86 %
Rwork0.1763 68152 -
obs0.1777 70162 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 219.15 Å2 / Biso mean: 38.3277 Å2 / Biso min: 14.24 Å2
Refinement stepCycle: final / Resolution: 2.7→48.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17042 0 0 288 17330
Biso mean---33.08 -
Num. residues----2138
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6204X-RAY DIFFRACTION5.125TORSIONAL
12B6204X-RAY DIFFRACTION5.125TORSIONAL
13C6204X-RAY DIFFRACTION5.125TORSIONAL
14D6204X-RAY DIFFRACTION5.125TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.770.32921540.23374677483197
2.77-2.840.28881290.225748194948100
2.84-2.930.25411470.223248324979100
2.93-3.020.30151450.224648004945100
3.02-3.130.27161330.221648374970100
3.13-3.250.28121420.199948294971100
3.25-3.40.25891410.191448554996100
3.4-3.580.24521420.192148434985100
3.58-3.810.23551470.16748725019100
3.81-4.10.21721380.149148795017100
4.1-4.510.17131460.140748795025100
4.51-5.160.15721440.134649075051100
5.16-6.50.18151470.170849815128100
6.5-48.80.20291550.166151425297100
Refinement TLS params.Method: refined / Origin x: 13.8502 Å / Origin y: 23.324 Å / Origin z: 29.9692 Å
111213212223313233
T0.1825 Å20.0206 Å20.0227 Å2-0.116 Å2-0.0271 Å2--0.1847 Å2
L0.2061 °20.0533 °2-0.0016 °2-0.0025 °2-0.0598 °2--0.156 °2
S0.0005 Å °-0.0098 Å °0.0162 Å °-0.0052 Å °0.0065 Å °-0.0076 Å °0.0125 Å °-0.0086 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA15 - 551
2X-RAY DIFFRACTION1allB15 - 542
3X-RAY DIFFRACTION1allC7 - 550
4X-RAY DIFFRACTION1allD15 - 543
5X-RAY DIFFRACTION1allS1 - 288

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