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- PDB-1p4x: Crystal structure of SarS protein from Staphylococcus Aureus -

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Basic information

Entry
Database: PDB / ID: 1p4x
TitleCrystal structure of SarS protein from Staphylococcus Aureus
Componentsstaphylococcal accessory regulator A homologue
KeywordsTRANSCRIPTION / winged-helix protein
Function / homology
Function and homology information


: / transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / DNA binding / cytoplasm
Similarity search - Function
Transcriptional regulator SarA/Rot / 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
HTH-type transcriptional regulator SarS / HTH-type transcriptional regulator SarS
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.2 Å
AuthorsLi, R. / Manna, A.C. / Dai, S. / Cheung, A.L. / Zhang, G.
CitationJournal: J.BACTERIOL. / Year: 2003
Title: Crystal structure of the SarS protein from Staphylococcus aureus
Authors: Li, R. / Manna, A.C. / Dai, S. / Cheung, A.L. / Zhang, G.
History
DepositionApr 24, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: staphylococcal accessory regulator A homologue


Theoretical massNumber of molelcules
Total (without water)29,9391
Polymers29,9391
Non-polymers00
Water2,108117
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.887, 84.887, 195.743
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein staphylococcal accessory regulator A homologue


Mass: 29938.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Plasmid: Pet14b / Production host: Escherichia coli (E. coli) / Strain (production host): Bcl-21 / References: UniProt: P0C0R2, UniProt: Q2G1N7*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 4

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Sample preparation

CrystalDensity Matthews: 3.4 Å3/Da / Density % sol: 63.82 %
Crystal growTemperature: 310 K / Method: vapor diffusion, hanging drop / pH: 8
Details: NaCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 37K
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115 mg/mlprotein1drop
25 mMbeta-mercaptoethanol1reservoir
3100 mMHEPES1reservoirpH7.5
43.5-4.0 M1reservoirNaCl

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU11.5418
SYNCHROTRONAPS 19-BM21
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS IV1IMAGE PLATENov 20, 2001Osma Mirror
ADSC QUANTUM 42CCDNov 10, 2001
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
211
ReflectionResolution: 2.2→20 Å / Num. all: 28880 / Num. obs: 28880 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 26 % / Biso Wilson estimate: 33.6 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.093 / Net I/σ(I): 41.59
Reflection shellResolution: 2.2→2.28 Å / % possible all: 98.2
Reflection
*PLUS
Num. obs: 22016 / % possible obs: 99.4 % / Num. measured all: 576575 / Rmerge(I) obs: 0.081
Reflection shell
*PLUS
% possible obs: 98.2 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MIR / Resolution: 2.2→19.96 Å / Rfactor Rfree error: 0.009 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.285 987 5 %RANDOM
Rwork0.24 ---
obs0.24 19644 89.4 %-
all-22016 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.2254 Å2 / ksol: 0.355224 e/Å3
Displacement parametersBiso mean: 51.1 Å2
Baniso -1Baniso -2Baniso -3
1-4.87 Å25.92 Å20 Å2
2--4.87 Å20 Å2
3----9.74 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2104 0 0 117 2221
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d19.7
X-RAY DIFFRACTIONc_improper_angle_d0.76
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.396 126 5 %
Rwork0.328 2386 -
obs--70.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CARBOHYDRATE.PARAM
X-RAY DIFFRACTION3WATER.PARAM
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 20 Å / Num. reflection obs: 21142 / Rfactor Rfree: 0.282 / Rfactor Rwork: 0.245
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.76

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