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- PDB-3l7w: The Crystal Structure of smu.1704 from Streptococcus mutans UA159 -

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Basic information

Entry
Database: PDB / ID: 3l7w
TitleThe Crystal Structure of smu.1704 from Streptococcus mutans UA159
ComponentsPutative uncharacterized protein SMU.1704
KeywordsTRANSCRIPTION / PadR / transcriptional factor
Function / homology
Function and homology information


: / Transcription regulator PadR, N-terminal / Transcriptional regulator PadR-like family / 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
Transcription regulator PadR N-terminal domain-containing protein
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsSu, X.-D. / Liu, X. / Fu, T.M.
CitationJournal: TO BE PUBLISHED
Title: The Crystal Structure of smu.1704 from Streptococcus mutans UA159
Authors: Su, X.-D. / Liu, X. / Fu, T.M.
History
DepositionDec 29, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein SMU.1704


Theoretical massNumber of molelcules
Total (without water)12,8041
Polymers12,8041
Non-polymers00
Water1,892105
1
A: Putative uncharacterized protein SMU.1704

A: Putative uncharacterized protein SMU.1704


Theoretical massNumber of molelcules
Total (without water)25,6092
Polymers25,6092
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_544x,x-y-1,-z-1/61
Buried area3790 Å2
ΔGint-30 kcal/mol
Surface area10950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.070, 57.070, 174.920
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-116-

HOH

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Components

#1: Protein Putative uncharacterized protein SMU.1704


Mass: 12804.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: UA159 / Gene: SMU.1704 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8DSR7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.21 Å3/Da / Density % sol: 61.69 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES pH7.5, 3.0M Sodium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 19, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 9236 / Num. obs: 9136 / % possible obs: 98.9 % / Observed criterion σ(I): 1 / Biso Wilson estimate: 37.87 Å2
Reflection shellResolution: 2.2→2.3 Å / % possible all: 93.8

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Processing

SoftwareName: PHENIX / Version: (phenix.refine) / Classification: refinement
RefinementMethod to determine structure: SAD / Resolution: 2.2→18.851 Å / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.789 / SU ML: 0.33 / σ(F): 1.99 / Phase error: 25.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2694 914 10 %
Rwork0.2041 8222 -
obs0.2106 9136 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.718 Å2 / ksol: 0.351 e/Å3
Displacement parametersBiso max: 98.06 Å2 / Biso mean: 41.869 Å2 / Biso min: 19.46 Å2
Baniso -1Baniso -2Baniso -3
1-6.143 Å20 Å2-0 Å2
2--6.143 Å20 Å2
3----12.286 Å2
Refinement stepCycle: LAST / Resolution: 2.2→18.851 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms870 0 0 105 975
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009896
X-RAY DIFFRACTIONf_angle_d1.2061211
X-RAY DIFFRACTIONf_dihedral_angle_d15.847323
X-RAY DIFFRACTIONf_chiral_restr0.073136
X-RAY DIFFRACTIONf_plane_restr0.006144
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.31580.39121180.29661066X-RAY DIFFRACTION95
2.3158-2.46060.26891290.23471155X-RAY DIFFRACTION100
2.4606-2.65010.26331270.19521149X-RAY DIFFRACTION100
2.6501-2.9160.26621300.20821168X-RAY DIFFRACTION100
2.916-3.33590.28241300.20331177X-RAY DIFFRACTION100
3.3359-4.19520.22591350.16561201X-RAY DIFFRACTION100
4.1952-18.85150.2341450.17081306X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 4.2004 Å / Origin y: -23.8046 Å / Origin z: -3.3915 Å
111213212223313233
T0.1036 Å2-0.0589 Å20.0196 Å2-0.2866 Å2-0.026 Å2--0.1907 Å2
L0.1964 °2-0.2776 °2-0.6795 °2-0.8546 °21.2015 °2--2.2058 °2
S0.0421 Å °-0.0737 Å °-0.0645 Å °-0.0473 Å °-0.0502 Å °0.0555 Å °-0.1568 Å °0.0695 Å °-0.0001 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 106
2X-RAY DIFFRACTION1allA1 - 113

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