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- PDB-3kp3: Staphylococcus epidermidis in complex with ampicillin -

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Basic information

Entry
Database: PDB / ID: 3kp3
TitleStaphylococcus epidermidis in complex with ampicillin
ComponentsTranscriptional regulator TcaR
KeywordsTRANSCRIPTION REGULATOR/ANTIBIOTIC / Multiple drug resistance / biofilm / transcription regulation / DNA binding / antibiotics / DNA-binding / Transcription / TRANSCRIPTION REGULATOR-ANTIBIOTIC complex
Function / homology
Function and homology information


response to stress / 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 ...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
Chem-AIC / Transcriptional regulator TcaR
Similarity search - Component
Biological speciesStaphylococcus epidermidis RP62A (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)35,4554
Polymers34,7562
Non-polymers6992
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6260 Å2
ΔGint-35 kcal/mol
Surface area16120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.033, 108.033, 49.760
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: pET 21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5HLN6
#2: Chemical ChemComp-AIC / (2S,5R,6R)-6-{[(2R)-2-AMINO-2-PHENYLETHANOYL]AMINO}-3,3-DIMETHYL-7-OXO-4-THIA-1-AZABICYCLO[3.2.0]HEPTANE-2-CARBOXYLIC ACID / AMPICILLIN / D(-)-ALPHA-AMINOBENZYLPENICILLIN / 6-[D(-)-ALPHA-AMINOPHENYLLACETAMIDO]PENICILLANIC ACID


Mass: 349.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H19N3O4S / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 49 %
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: BL13C1 / Wavelength: 0.97622 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 24, 2009 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. all: 5615 / Num. obs: 5615 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 19.2
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.453 / Mean I/σ(I) obs: 2.9 / Num. unique all: 548 / % possible all: 88.3

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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: 3.2→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.274 297 -RANDOM
Rwork0.247 ---
all-5615 --
obs-5348 95.3 %-
Displacement parametersBiso mean: 57.15 Å2
Refine analyzeLuzzati coordinate error obs: 0.4 Å / Luzzati sigma a obs: 0.54 Å
Refinement stepCycle: LAST / Resolution: 3.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2191 0 48 83 2322
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
LS refinement shellResolution: 3.2→3.31 Å
RfactorNum. reflection% reflection
Rfree0.359 26 -
Rwork0.316 --
obs-499 88.3 %

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