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- PDB-4em1: staphylococcus aureus MarR native -

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Basic information

Entry
Database: PDB / ID: 4em1
Titlestaphylococcus aureus MarR native
ComponentsUncharacterized HTH-type transcriptional regulator SAR2349
KeywordsTRANSCRIPTION / marR family proteins / MarR
Function / homology
Function and homology information


response to stress / DNA-binding transcription factor activity / DNA binding
Similarity search - Function
Transcriptional regulator MarR-type, conserved site / MarR-type HTH domain signature. / : / MarR family / 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 ...Transcriptional regulator MarR-type, conserved site / MarR-type HTH domain signature. / : / MarR family / 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
Uncharacterized HTH-type transcriptional regulator SAR2349
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsChang, Y.M. / Chen, C.K.-M. / Wang, A.H.-J.
CitationJournal: To be Published
Title: Staphylococcus aureus MarR native
Authors: Chang, Y.M. / Chen, C.K.-M. / Wang, A.H.-J.
History
DepositionApr 11, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized HTH-type transcriptional regulator SAR2349


Theoretical massNumber of molelcules
Total (without water)20,6641
Polymers20,6641
Non-polymers00
Water1,856103
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Uncharacterized HTH-type transcriptional regulator SAR2349

A: Uncharacterized HTH-type transcriptional regulator SAR2349


Theoretical massNumber of molelcules
Total (without water)41,3272
Polymers41,3272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5260 Å2
ΔGint-36 kcal/mol
Surface area16350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.122, 75.218, 109.427
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Uncharacterized HTH-type transcriptional regulator SAR2349 / Transcriptional regulator MarR


Mass: 20663.557 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: MRSA252 / Gene: SAR2349 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6GEG9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 1.8 Å3/Da / Density % sol: 31.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% 5000 MME, 0.2M LiSO4, 0.1M Tris PH 8.0, 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 24, 2010 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→22 Å / Num. obs: 3179 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 16.8
Reflection shellResolution: 2.9→3.03 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 3.6 / Num. unique all: 573 / % possible all: 99.3

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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: PDB ENTRY 4EM2

4em2


Resolution: 3→22 Å / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2935 135 4.2 %random
Rwork0.2693 2910 --
obs-3045 95.8 %-
Solvent computationBsol: 171.83 Å2
Displacement parametersBiso max: 72.65 Å2 / Biso mean: 38.9912 Å2 / Biso min: 1 Å2
Baniso -1Baniso -2Baniso -3
1-4.193 Å20 Å20 Å2
2--0.981 Å20 Å2
3----5.174 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å / Luzzati sigma a obs: 0.33 Å
Refinement stepCycle: LAST / Resolution: 3→22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1183 0 0 103 1286
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.2341.5
X-RAY DIFFRACTIONc_scbond_it1.5482
X-RAY DIFFRACTIONc_mcangle_it2.0792
X-RAY DIFFRACTIONc_scangle_it2.1172.5
LS refinement shellResolution: 3→3.14 Å /
Num. reflection% reflection
obs282 96.6 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2dna-rna_rep.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4ion.param

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