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- PDB-4u88: Structure of the DNA-Binding Domain of the Response Regulator Sae... -

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Basic information

Entry
Database: PDB / ID: 4u88
TitleStructure of the DNA-Binding Domain of the Response Regulator SaeR from Staphylococcus aureus
ComponentsTranscriptional regulator SaeR
KeywordsDNA BINDING PROTEIN / DNA-binding protein / transcriptional
Function / homology
Function and homology information


phosphorelay signal transduction system / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcriptional regulator SaeR / :
Similarity search - Component
Biological speciesStaphylococcus aureus USA300-ISMMS1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.355 Å
AuthorsLiu, J.S. / Huang, C.H. / Yang, C.S. / Chen, S.C. / Chen, Y.
CitationJournal: To Be Published
Title: Structure of the DNA-Binding Domain of the Response Regulator SaeR from Staphylococcus aureus
Authors: Liu, J.S. / Huang, C.H. / Yang, C.S. / Chen, S.C. / Chen, Y.
History
DepositionAug 1, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator SaeR
B: Transcriptional regulator SaeR


Theoretical massNumber of molelcules
Total (without water)26,3242
Polymers26,3242
Non-polymers00
Water64936
1
A: Transcriptional regulator SaeR


Theoretical massNumber of molelcules
Total (without water)13,1621
Polymers13,1621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcriptional regulator SaeR


Theoretical massNumber of molelcules
Total (without water)13,1621
Polymers13,1621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.966, 61.024, 116.759
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Transcriptional regulator SaeR / SaeR


Mass: 13161.806 Da / Num. of mol.: 2 / Fragment: UNP residues 128-228
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus USA300-ISMMS1 (bacteria)
Gene: AZ30_03680 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: W6DZ35, UniProt: A0A0M3KKX4*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.16 Å3/Da / Density % sol: 43.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 5% v/v Tacsimate, pH 7.0, 0.1M HEPES pH 7.0, 10% w/v Polyethylene glycol monomethyl ether 5000

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→30 Å / Num. obs: 9992 / % possible obs: 99.6 % / Redundancy: 9.4 % / Net I/σ(I): 19.7

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IXA

4ixa


Resolution: 2.355→29.521 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 29.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2643 996 10.01 %
Rwork0.1941 --
obs0.201 9951 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.355→29.521 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1615 0 0 36 1651
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091649
X-RAY DIFFRACTIONf_angle_d1.1632230
X-RAY DIFFRACTIONf_dihedral_angle_d13.259604
X-RAY DIFFRACTIONf_chiral_restr0.046253
X-RAY DIFFRACTIONf_plane_restr0.006273
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3545-2.47860.36321360.25351217X-RAY DIFFRACTION96
2.4786-2.63380.30731370.22781245X-RAY DIFFRACTION100
2.6338-2.8370.31351410.22771258X-RAY DIFFRACTION100
2.837-3.12220.31791410.21861267X-RAY DIFFRACTION100
3.1222-3.57330.2921430.21311295X-RAY DIFFRACTION100
3.5733-4.49950.21741430.16751291X-RAY DIFFRACTION100
4.4995-29.5230.23051550.17081382X-RAY DIFFRACTION100

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