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- PDB-4em2: seleno-methionine staphylococcus aureus MarR in complex with sali... -

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Basic information

Entry
Database: PDB / ID: 4em2
Titleseleno-methionine staphylococcus aureus MarR in complex with salicylate
ComponentsUncharacterized HTH-type transcriptional regulator SAR2349
KeywordsTRANSCRIPTION / marR family proteins / MarR / salicylate
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
2-HYDROXYBENZOIC ACID / Uncharacterized HTH-type transcriptional regulator SAR2349
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.08 Å
AuthorsChang, Y.M. / Ko, T.-P. / Chen, C.K.-M. / Wang, A.H.-J.
CitationJournal: To be Published
Title: Staphylococcus aureus MarR complexes
Authors: Chang, Y.M. / Ko, T.-P. / 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 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Uncharacterized HTH-type transcriptional regulator SAR2349
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4087
Polymers20,6641
Non-polymers7456
Water3,729207
1


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

A: Uncharacterized HTH-type transcriptional regulator SAR2349
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,81614
Polymers41,3272
Non-polymers1,48912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area9190 Å2
ΔGint-70 kcal/mol
Surface area15150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.191, 84.191, 61.452
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-614-

HOH

21A-719-

HOH

31A-721-

HOH

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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: pET32 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6GEG9
#2: Chemical
ChemComp-SAL / 2-HYDROXYBENZOIC ACID / SALICYLIC ACID / Salicylic acid


Mass: 138.121 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H6O3
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 3.04 Å3/Da / Density % sol: 59.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 38% 5000 MME, 1M LiSO4, 0.1M Tris PH 8.5 , VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL12B211
SYNCHROTRONPhoton Factory BL-5A20.97877, 0.97936, 0.96413
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDDec 19, 2009
ADSC QUANTUM 3152CCDNov 1, 2008
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1graphiteSINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.978771
30.979361
40.964131
ReflectionResolution: 2.08→30 Å / Num. all: 15436 / Num. obs: 15461 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 39.1
Reflection shellResolution: 2.08→2.15 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.536 / Mean I/σ(I) obs: 4.6 / Num. unique all: 1515 / % possible all: 99.9

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.08→30 Å / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.272 735 4.8 %random
Rwork0.201 ---
all-15436 --
obs-14801 95.9 %-
Solvent computationBsol: 43.5916 Å2
Displacement parametersBiso max: 95.75 Å2 / Biso mean: 42.03 Å2 / Biso min: 18.45 Å2
Baniso -1Baniso -2Baniso -3
1--2.616 Å2-3.126 Å20 Å2
2---2.616 Å20 Å2
3---5.232 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å / Luzzati sigma a obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 2.08→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1234 0 50 207 1491
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.021
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_mcbond_it1.5561.5
X-RAY DIFFRACTIONc_scbond_it2.5892
X-RAY DIFFRACTIONc_mcangle_it2.5222
X-RAY DIFFRACTIONc_scangle_it3.9492.5
LS refinement shellResolution: 2.08→2.15 Å /
Num. reflection% reflection
Rfree63 -
obs1367 90.5 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4ligand.param

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