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- PDB-5kcb: The structure of SAV2435 bound to ethidium bromide -

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Basic information

Entry
Database: PDB / ID: 5kcb
TitleThe structure of SAV2435 bound to ethidium bromide
ComponentsSA2223 protein
KeywordsUNKNOWN FUNCTION / GyrI-like domatin / multi-drug recognition
Function / homology
Function and homology information


Integron-associated effector binding protein / Integron-associated effector binding protein / Bacterial transcription activator, effector binding / Bacterial transcription activator, effector 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
ETHIDIUM / SA2223 protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.101 Å
AuthorsMoreno, A. / Wade, H.
Funding support United States, 2items
OrganizationGrant numberCountry
Arnold and Mabel Beckman Young Investigator Award United States
National Science Foundation (NSF, United States)MCB-0953430 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 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: 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 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SA2223 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3515
Polymers18,7481
Non-polymers6034
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-34 kcal/mol
Surface area9630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.720, 73.720, 68.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein SA2223 protein


Mass: 18748.146 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain N315) (bacteria)
Strain: N315 / Gene: SA2223 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H3JRN6
#2: Chemical ChemComp-ET / ETHIDIUM


Mass: 314.404 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H20N3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O

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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: 2.48 Å3/Da / Density % sol: 50.47 %
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 SATURN 944+ / Detector: CCD / Date: Sep 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.101→32.462 Å / Num. obs: 11441 / % possible obs: 99.5 % / Redundancy: 2 % / Net I/σ(I): 38.04

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2.101→32.462 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.5
RfactorNum. reflection% reflection
Rfree0.2194 552 4.83 %
Rwork0.1989 --
obs0.1999 11432 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.101→32.462 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1317 0 39 78 1434
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051387
X-RAY DIFFRACTIONf_angle_d0.9091882
X-RAY DIFFRACTIONf_dihedral_angle_d14.392490
X-RAY DIFFRACTIONf_chiral_restr0.037195
X-RAY DIFFRACTIONf_plane_restr0.004239
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1011-2.31250.27361450.23782590X-RAY DIFFRACTION98
2.3125-2.6470.28031350.2282691X-RAY DIFFRACTION100
2.647-3.33440.23511320.21452725X-RAY DIFFRACTION100
3.3344-32.46610.18341400.17552874X-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)
10.846-0.56910.20533.32140.25491.86580.13450.09170.0871-0.1689-0.17330.13780.05750.1460.04050.29840.0324-0.05420.2339-0.04020.2839-19.49091.79624.2265
22.233-0.41010.29352.62760.4082.95680.08750.4034-0.1989-0.4207-0.07220.00180.23820.28860.05030.32860.0604-0.01360.2585-0.03870.2232-17.172311.6739-0.2553
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 77 )
2X-RAY DIFFRACTION2chain 'A' and (resid 78 through 166 )

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