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- PDB-8oo2: ChdA complex with amido-chelocardin -

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Basic information

Entry
Database: PDB / ID: 8oo2
TitleChdA complex with amido-chelocardin
ComponentsPutative transcriptional regulator
KeywordsTRANSCRIPTION / ChdA complex with amido-chelocardin / Tet-R family like regulator / atypical tetracycline
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / response to antibiotic / negative regulation of DNA-templated transcription / metal ion binding
Similarity search - Function
Tetracycline transcriptional regulator, TetR / Tetracycline repressor TetR, C-terminal / Tetracyclin repressor-like, C-terminal domain / DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / : / Tetracyclin repressor-like, C-terminal domain superfamily / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily
Similarity search - Domain/homology
2-carboxamido-2-deacetyl-chelocardin / Putative transcriptional regulator
Similarity search - Component
Biological speciesAmycolatopsis sulphurea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsKoehnke, J. / Sikandar, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)KO4116_3_1 Germany
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2023
Title: Revision of the Absolute Configurations of Chelocardin and Amidochelocardin.
Authors: Sikandar, A. / Popoff, A. / Jumde, R.P. / Mandi, A. / Kaur, A. / Elgaher, W.A.M. / Rosenberger, L. / Huttel, S. / Jansen, R. / Hunter, M. / Kohnke, J. / Hirsch, A.K.H. / Kurtan, T. / Muller, R.
History
DepositionApr 4, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 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.journal_volume / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative transcriptional regulator
B: Putative transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8756
Polymers42,0022
Non-polymers8734
Water3,369187
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint-37 kcal/mol
Surface area16350 Å2
Unit cell
Length a, b, c (Å)44.580, 82.780, 99.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative transcriptional regulator / TetR family transcriptional regulator


Mass: 21001.045 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amycolatopsis sulphurea (bacteria) / Gene: chdA, ATK36_5244 / Production host: Escherichia coli (E. coli) / References: UniProt: V9XTV0
#2: Chemical ChemComp-AV8 / 2-carboxamido-2-deacetyl-chelocardin / (4S,4aR,12aR)-4-azanyl-6,9-dimethyl-3,10,11,12a-tetrakis(oxidanyl)-1,12-bis(oxidanylidene)-4a,5-dihydro-4H-tetracene-2-carboxamide / amido-chelocardin


Mass: 412.393 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H20N2O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.4 Å3/Da / Density % sol: 48.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 16% (w/v) PEG 8000, 0.2 M sodium acetate and 0.1 M sodium cacodylate pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.779 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.779 Å / Relative weight: 1
ReflectionResolution: 1.85→42.78 Å / Num. obs: 32227 / % possible obs: 99.5 % / Redundancy: 11.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rrim(I) all: 0.062 / Net I/σ(I): 24.5
Reflection shellResolution: 1.85→1.9 Å / Rmerge(I) obs: 0.322 / Num. unique obs: 2213 / CC1/2: 0.927

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Processing

Software
NameVersionClassification
PHENIX(1.19.1_4122: ???)refinement
xia2data reduction
Aimlessdata scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→42.78 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 21.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2125 1608 5 %
Rwork0.1742 --
obs0.1761 32171 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→42.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2694 0 62 187 2943
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132814
X-RAY DIFFRACTIONf_angle_d0.9273827
X-RAY DIFFRACTIONf_dihedral_angle_d4.614418
X-RAY DIFFRACTIONf_chiral_restr0.057431
X-RAY DIFFRACTIONf_plane_restr0.017489
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.910.29661260.24622599X-RAY DIFFRACTION95
1.91-1.980.25941380.21662722X-RAY DIFFRACTION99
1.98-2.060.25581520.19072755X-RAY DIFFRACTION100
2.06-2.150.21221490.16932749X-RAY DIFFRACTION100
2.15-2.260.23031350.1632772X-RAY DIFFRACTION100
2.26-2.410.18341520.16192763X-RAY DIFFRACTION100
2.41-2.590.19251530.16862791X-RAY DIFFRACTION100
2.59-2.850.20981450.17062788X-RAY DIFFRACTION100
2.85-3.270.20231420.17682807X-RAY DIFFRACTION100
3.27-4.110.19411530.15572835X-RAY DIFFRACTION100
4.11-42.780.22091630.17982982X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
19.40386.20155.56029.28436.95658.2076-0.06070.02140.56730.30580.02020.4997-0.15680.1103-0.02570.1585-0.01320.03220.23410.01460.1821-14.09567.094312.0221
23.8639-2.4938-0.77584.71514.33298.92470.0172-0.0530.4887-0.3933-0.07610.0856-0.9729-0.44130.04060.34240.03830.01780.23590.08210.2899-15.946114.44586.9881
38.4252-6.47664.37785.7505-5.65039.13940.0823-0.08170.2062-0.07920.0327-0.05870.09120.2959-0.07420.15280.00120.02610.2053-0.03980.1334-4.51332.16237.8895
42.7418-0.9909-0.20373.6954-0.01561.5541-0.3245-0.8918-0.14010.35440.3209-0.25120.34250.1364-0.08240.2130.06730.0060.24750.0160.14533.0879-11.66137.211
53.7979-0.55-0.11013.06060.23171.91530.005-0.51410.41160.07540.0519-0.106-0.14230.2567-0.08390.16030.00170.03770.2251-0.04450.1633-2.07732.76224.3593
67.1539-3.479-2.95554.8377-2.79747.5962-0.0348-1.44590.3160.47340.0569-0.9991-0.22150.23630.20840.1935-0.0393-0.07710.37260.04460.354916.4175-5.56396.7208
76.24091.20075.05273.46021.32118.00450.1530.1122-0.27920.069-0.0527-0.23110.06030.0332-0.06670.11820.0110.02320.10790.02690.11733.4636-4.9219-3.0492
86.58571.18714.64532.51870.46517.0149-0.10470.0828-0.088-0.09520.0119-0.02940.3315-0.21550.01090.2589-0.02890.02950.16050.00040.17630.7258-15.9853-6.1593
94.3032.3251.75375.29113.37464.847-0.24270.19520.2719-0.05680.23230.578-0.5957-0.53870.14620.43570.13610.00090.50740.10750.26-18.18370.1375-28.1821
102.28082.57430.27835.45712.01076.9267-0.5371-0.36991.23570.2308-0.24651.1399-0.7721-1.85330.4570.63140.32720.00870.81770.01330.5513-23.85093.7952-20.3532
117.6323-1.21612.45032.082-0.52174.945-0.0630.3584-0.44660.05670.14940.25220.0746-0.7357-0.12280.2679-0.0243-0.02050.46430.06460.2231-12.5878-7.7981-25.2688
127.0695-4.8798-1.01927.96672.44022.77440.15210.55560.3762-0.3037-0.0254-0.5443-0.33650.4204-0.25760.2204-0.03410.04480.34560.03120.18794.5856-6.687-20.7671
135.5505-1.00490.15527.9221.35583.1401-0.0421-0.17990.2945-0.01120.2630.1877-0.1069-0.2899-0.00240.2106-0.0154-0.0180.34760.04280.1751-10.7978-3.3603-16.7154
144.5931-5.74755.11667.9311-4.81988.77540.42580.8174-1.0995-0.8139-0.1649-0.00920.92570.1282-0.32310.4253-0.01840.01470.241-0.06830.2658-1.0872-21.4593-23.7435
152.8781-0.9578-1.21327.92276.79148.2162-0.05190.0084-0.1114-0.02570.09190.19230.1139-0.0994-0.09430.1191-0.0088-0.00290.20970.06080.1094-0.6656-11.283-12.6331
166.2651-3.9825-0.59138.18253.55477.0982-0.09030.0040.5046-0.47890.2472-0.4514-0.31770.2123-0.12310.1496-0.0274-0.00730.3323-0.00070.21158.4962-6.4627-10.8226
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 19 )
2X-RAY DIFFRACTION2chain 'A' and (resid 20 through 46 )
3X-RAY DIFFRACTION3chain 'A' and (resid 47 through 67 )
4X-RAY DIFFRACTION4chain 'A' and (resid 68 through 92 )
5X-RAY DIFFRACTION5chain 'A' and (resid 93 through 116 )
6X-RAY DIFFRACTION6chain 'A' and (resid 117 through 126 )
7X-RAY DIFFRACTION7chain 'A' and (resid 127 through 148 )
8X-RAY DIFFRACTION8chain 'A' and (resid 149 through 181 )
9X-RAY DIFFRACTION9chain 'B' and (resid 1 through 19 )
10X-RAY DIFFRACTION10chain 'B' and (resid 20 through 33 )
11X-RAY DIFFRACTION11chain 'B' and (resid 34 through 74 )
12X-RAY DIFFRACTION12chain 'B' and (resid 75 through 92 )
13X-RAY DIFFRACTION13chain 'B' and (resid 93 through 106 )
14X-RAY DIFFRACTION14chain 'B' and (resid 107 through 126 )
15X-RAY DIFFRACTION15chain 'B' and (resid 127 through 148 )
16X-RAY DIFFRACTION16chain 'B' and (resid 149 through 181 )

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