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- PDB-2frh: Crystal Structure of Sara, A Transcription Regulator From Staphyl... -

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Basic information

Entry
Database: PDB / ID: 2frh
TitleCrystal Structure of Sara, A Transcription Regulator From Staphylococcus Aureus
ComponentsStaphylococcal accessory regulator A
KeywordsTRANSCRIPTION / WINGED-HELIX PROTEIN / DIVALENT METAL BINDING
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding / metal ion binding / cytoplasm
Similarity search - Function
Transcriptional regulator SarA/Rot / Transcriptional regulator SarA/Rot / 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 / MIR / Resolution: 2.5 Å
AuthorsLiu, Y. / Manna, A.C. / Ingavale, S. / 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 19, 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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: Staphylococcal accessory regulator A
B: Staphylococcal accessory regulator A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1274
Polymers30,0472
Non-polymers802
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-38 kcal/mol
Surface area14890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.338, 65.338, 237.289
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Staphylococcal accessory regulator A / SARA


Mass: 15023.280 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: sarA / Production host: Escherichia coli (E. coli) / References: UniProt: Q7A1N5
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.44 %
Crystal growpH: 6.5
Details: PEG 4000, PH 6.5, VAPOR DIFFUSION, HANGING DROP AT 277K, pH 6.50

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1
DetectorType: PRINCETON 2K / Detector: CCD / Date: Sep 1, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 10107 / % possible obs: 89.7 % / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 37.9 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 33

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS0.9refinement
RefinementMethod to determine structure: MIR / Resolution: 2.5→19.5 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 284287.65 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.302 450 5.3 %RANDOM
Rwork0.266 ---
obs0.266 8562 77.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.24 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 77.6 Å2
Baniso -1Baniso -2Baniso -3
1-3.49 Å210.89 Å20 Å2
2--3.49 Å20 Å2
3----6.97 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.5→19.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2112 0 2 0 2114
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.71
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: 2.5→2.66 Å / Rfactor Rfree error: 0.091 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.395 19 4.7 %
Rwork0.318 387 -
obs--22.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CARBOHYDRATE.PARAM
X-RAY DIFFRACTION3WATER.PARAM
X-RAY DIFFRACTION4ION.PARAM

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