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- PDB-5kax: The structure of CTR107 protein bound to RHODAMINE 6G -

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Basic information

Entry
Database: PDB / ID: 5kax
TitleThe structure of CTR107 protein bound to RHODAMINE 6G
ComponentsCTR107 protein
KeywordsUNKNOWN FUNCTION / GyrI-like domatin / multi-drug recognition
Function / homology
Function and homology information


Bacterial transcription activator, effector binding / Bacterial transcription activator, effector binding domain / GyrI-like small molecule binding domain / Multidrug-efflux Transporter 1 Regulator Bmrr; Chain A / Regulatory factor, effector binding domain / GyrI-like small molecule binding domain / Regulatory factor, effector binding domain superfamily / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
RHODAMINE 6G / Bacterial transcription activator effector binding domain-containing protein
Similarity search - Component
Biological speciesChlorobium tepidum (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsMoreno, A. / Wade, H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-0953430 United States
Arnold and Mabel Beckman Young Investigator Award United States
CitationJournal: Biochemistry / Year: 2016
Title: Solution Binding and Structural Analyses Reveal Potential Multidrug Resistance Functions for SAV2435 and CTR107 and Other GyrI-like Proteins.
Authors: Moreno, A. / Froehlig, J.R. / Bachas, S. / Gunio, D. / Alexander, T. / Vanya, A. / Wade, H.
History
DepositionJun 2, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CTR107 protein
B: CTR107 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6809
Polymers36,3332
Non-polymers1,3487
Water3,927218
1
A: CTR107 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0707
Polymers18,1661
Non-polymers9046
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CTR107 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6102
Polymers18,1661
Non-polymers4441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.958, 71.958, 146.870
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein CTR107 protein


Mass: 18166.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlorobium tepidum (strain ATCC 49652 / DSM 12025 / NBRC 103806 / TLS) (bacteria)
Strain: ATCC 49652 / DSM 12025 / NBRC 103806 / TLS / Gene: CT0179 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8KFZ1
#2: Chemical ChemComp-RHQ / RHODAMINE 6G


Mass: 443.557 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H31N2O3
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O
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: 3.02 Å3/Da / Density % sol: 59.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 2.4 M ammonium sulfate, 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 22, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→47.52 Å / Num. obs: 27525 / % possible obs: 94.93 % / Redundancy: 4.4 % / Net I/σ(I): 23.76

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2→47.515 Å / Cross valid method: FREE R-VALUE / σ(F): 2.34 / Phase error: 26.03
RfactorNum. reflection% reflection
Rfree0.1793 1415 5.14 %
Rwork0.1412 --
obs0.1462 27525 94.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→47.515 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2376 0 96 218 2690
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142552
X-RAY DIFFRACTIONf_angle_d1.313466
X-RAY DIFFRACTIONf_dihedral_angle_d15.485913
X-RAY DIFFRACTIONf_chiral_restr0.054361
X-RAY DIFFRACTIONf_plane_restr0.005447
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0013-2.07260.31171590.28012677X-RAY DIFFRACTION93
2.0726-2.15520.29351460.24022639X-RAY DIFFRACTION93
2.1552-2.25290.21881290.21782692X-RAY DIFFRACTION93
2.2529-2.37110.24591280.20812643X-RAY DIFFRACTION92
2.3711-2.51880.21341390.19622583X-RAY DIFFRACTION90
2.5188-2.71190.23571380.18372596X-RAY DIFFRACTION90
2.7119-2.98220.19221210.16192615X-RAY DIFFRACTION90
2.9822-3.40790.18581550.13612560X-RAY DIFFRACTION89
3.4079-4.27170.14331530.10092536X-RAY DIFFRACTION88
4.2717-13.65720.13991370.0982491X-RAY DIFFRACTION85
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)
10.6482-0.0790.48430.5070.26590.50620.00520.1092-0.3943-0.1305-0.05230.1694-0.3920.4048-0.00030.4158-0.0573-0.02630.4079-0.03470.4119-24.168721.4946-14.3957
20.7657-0.40660.11940.36080.08380.1783-0.17750.14990.1123-0.11950.1983-0.471-0.0567-0.16670.00020.3269-0.01720.01010.3403-0.03940.3435-6.129434.0276-4.0246
30.6880.28340.15950.44590.25590.1913-0.02720.0431-0.333-0.13080.0635-0.62120.11180.37690.00010.3049-0.00540.03980.3833-0.03890.42990.799826.0195-2.7927
42.87130.7545-0.41171.74131.71742.18730.0479-0.0854-0.1850.02460.0132-0.10420.1787-0.1318-0.00130.2735-0.0016-0.00890.3171-0.01050.2889-8.944927.5948-1.0693
51.1303-0.57090.8661.1109-0.02220.91390.11820.12180.2104-0.3477-0.13180.237-0.0963-0.1091-0.00020.3551-0.015-0.01420.3667-0.01930.362-20.367528.257-15.4785
61.090.69890.73471.6749-0.52171.4017-0.2430.2466-0.12480.1242-0.1103-0.01360.0517-0.0077-0.00010.2875-0.05860.01690.4077-0.04270.2934-12.759222.9191-14.3269
70.747-0.4113-0.40910.3711-0.07630.46050.0386-0.0983-0.15250.18090.21340.3217-0.1730.3867-0.00130.3461-0.01920.04230.4421-0.03310.4541-26.86431.164417.2567
81.05130.1548-0.61941.16090.60720.9197-0.0049-0.1520.3031-0.00760.0117-0.2104-0.10650.2127-0.00020.3205-0.0314-0.01320.2916-0.03240.3702-10.249147.97536.773
92.25841.0903-1.061.98731.03042.1243-0.0046-0.1367-0.0756-0.17560.03330.03990.1110.00850.00040.2695-0.02970.04080.27310.00030.2777-13.430641.37138.5363
101.31440.1771-0.62192.3971-0.03082.7008-0.0505-0.0837-0.13940.2182-0.09270.01680.17380.07610.00040.2637-0.0120.00710.297-0.01930.3272-19.135136.567114.5416
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 17 )
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 30 )
3X-RAY DIFFRACTION3chain 'A' and (resid 31 through 49 )
4X-RAY DIFFRACTION4chain 'A' and (resid 50 through 94 )
5X-RAY DIFFRACTION5chain 'A' and (resid 95 through 135 )
6X-RAY DIFFRACTION6chain 'A' and (resid 136 through 158 )
7X-RAY DIFFRACTION7chain 'B' and (resid 2 through 17 )
8X-RAY DIFFRACTION8chain 'B' and (resid 18 through 49 )
9X-RAY DIFFRACTION9chain 'B' and (resid 50 through 76 )
10X-RAY DIFFRACTION10chain 'B' and (resid 77 through 158 )

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