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- PDB-3kp4: Staphylococcus epidermidis TcaR in complex with methicillin -

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Basic information

Entry
Database: PDB / ID: 3kp4
TitleStaphylococcus epidermidis TcaR in complex with methicillin
ComponentsTranscriptional regulator TcaR
KeywordsTRANSCRIPTION REGULATOR/ANTIBIOTIC / Multiple drug resistance / biofilm / transcription regulation / DNA binding / antibiotics / Transcription / TRANSCRIPTION REGULATOR-ANTIBIOTIC complex
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding
Similarity search - Function
MarR family / ArsR-like helix-turn-helix domain / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
methicillin / Transcriptional regulator TcaR
Similarity search - Component
Biological speciesStaphylococcus epidermidis RP62A (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å
AuthorsChang, Y.M. / Chen, C.K. / Wang, A.H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structural study of TcaR and its complexes with multiple antibiotics from Staphylococcus epidermidis.
Authors: Chang, Y.M. / Jeng, W.Y. / Ko, T.P. / Yeh, Y.J. / Chen, C.K. / Wang, A.H.
History
DepositionNov 15, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional regulator TcaR
B: Transcriptional regulator TcaR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5174
Polymers34,7562
Non-polymers7612
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5950 Å2
ΔGint-36 kcal/mol
Surface area15280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.547, 107.547, 49.406
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Transcriptional regulator TcaR


Mass: 17378.195 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus epidermidis RP62A (bacteria)
Strain: ATCC 35984 / Gene: SERP1949, SE_1937, tcaR / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5HLN6
#2: Chemical ChemComp-MII / methicillin


Mass: 380.416 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H20N2O6S / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.37 Å3/Da / Density % sol: 48.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Na-Hepes, pH 7.5, 8-14% PEG 4000, 10-13% 2-propanol precipitant, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 14, 2009 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.84→30 Å / Num. all: 7849 / Num. obs: 7703 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 60.17 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 22.7
Reflection shellResolution: 2.84→2.94 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3 / Num. unique all: 756 / % possible all: 86.8

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KP7

3kp7


Resolution: 2.84→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.256 403 -RANDOM
Rwork0.236 ---
all-7849 --
obs-7384 94.1 %-
Displacement parametersBiso mean: 60.17 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å / Luzzati sigma a obs: 0.42 Å
Refinement stepCycle: LAST / Resolution: 2.84→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2220 0 52 129 2401
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
LS refinement shellResolution: 2.84→2.94 Å
RfactorNum. reflection% reflection
Rfree0.331 36 -
Rwork0.279 --
obs-604 86.8 %

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