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- PDB-2fnp: Crystal structure of SarA -

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Basic information

Entry
Database: PDB / ID: 2fnp
TitleCrystal structure of SarA
ComponentsStaphylococcal accessory regulator A
KeywordsTRANSCRIPTION / wing-helix / DNA binding
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding / metal ion binding / cytoplasm
Similarity search - Function
Transcriptional regulator SarA/Rot / Winged helix DNA-binding domain / 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
Transcriptional regulator SarA
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLiu, Y. / Manna, A.C. / Pan, C.H. / Cheung, A.L. / Zhang, G.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Structural and function analyses of the global regulatory protein SarA from Staphylococcus aureus.
Authors: Liu, Y. / Manna, A.C. / Pan, C.H. / Kriksunov, I.A. / Thiel, D.J. / Cheung, A.L. / Zhang, G.
History
DepositionJan 11, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Staphylococcal accessory regulator A
B: Staphylococcal accessory regulator A


Theoretical massNumber of molelcules
Total (without water)29,5502
Polymers29,5502
Non-polymers00
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-32 kcal/mol
Surface area14020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.074, 64.758, 55.564
Angle α, β, γ (deg.)90.00, 117.73, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Staphylococcal accessory regulator A


Mass: 14775.021 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: strain MW2 / Gene: sarA / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL-21 / References: UniProt: Q7A1N5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.8 Å3/Da / Density % sol: 55.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.5
Details: 25% PEG 8000, 0.2M calcium chloride, 0.1M cacodylate, pH 6.5, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 52.074 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 9772 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 36 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 12
Reflection shellResolution: 2.6→2.69 Å / % possible all: 96

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
TRUNCATEdata reduction
AMoREphasing
CNS1.1refinement
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→39.17 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 732953.63 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.308 506 5.4 %RANDOM
Rwork0.285 ---
obs0.285 9426 92.5 %-
all-10177 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.5897 Å2 / ksol: 0.325189 e/Å3
Displacement parametersBiso mean: 70.5 Å2
Baniso -1Baniso -2Baniso -3
1--10.18 Å20 Å223.24 Å2
2---30.62 Å20 Å2
3---40.81 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.59 Å0.52 Å
Luzzati d res low-5 Å
Luzzati sigma a0.86 Å0.93 Å
Refinement stepCycle: LAST / Resolution: 2.6→39.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2052 0 0 11 2063
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.053 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.446 72 5.5 %
Rwork0.517 1236 -
obs--77.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top

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