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- PDB-3b2n: Crystal structure of DNA-binding response regulator, LuxR family,... -

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Basic information

Entry
Database: PDB / ID: 3b2n
TitleCrystal structure of DNA-binding response regulator, LuxR family, from Staphylococcus aureus
ComponentsUncharacterized protein Q99UF4
KeywordsTRANSCRIPTION / STRUCTURAL GENOMICS / PSI-2 / PROTEIN STRUCTURE INITIATIVE / New York SGX Research Center for Structural Genomics / NYSGXRC / Q99UF4 / DNA-binding / Transcription regulation
Function / homology
Function and homology information


phosphorelay signal transduction system / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily ...LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Similar to two-component response regulator / Similar to two-component response regulator
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / MAD / Resolution: 2.04 Å
AuthorsMalashkevich, V.N. / Toro, R. / Meyer, A.J. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of DNA-binding response regulator, LuxR family, from Staphylococcus aureus.
Authors: Malashkevich, V.N. / Toro, R. / Meyer, A.J. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionOct 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 21, 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: Uncharacterized protein Q99UF4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2262
Polymers15,2031
Non-polymers231
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.898, 67.898, 110.662
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Uncharacterized protein Q99UF4


Mass: 15202.530 Da / Num. of mol.: 1 / Fragment: Residues 2-124
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Mu50 / Gene: SAV1322 / Plasmid: BC-pSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Codon+RIL / References: UniProt: Q99UF4, UniProt: A0A0H3JRA8*PLUS
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.42 Å3/Da / Density % sol: 49.21 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Hepes pH 7.5, 1.4 M Sodium citrate, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 11, 2007 / Details: X29
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionRedundancy: 6.4 % / Av σ(I) over netI: 10.2 / Number: 101117 / Rmerge(I) obs: 0.083 / Χ2: 1.31 / D res high: 2.04 Å / D res low: 50 Å / Num. obs: 15739 / % possible obs: 86.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.395099.510.0461.6558.2
3.494.3910010.0652.0778.3
3.053.4910010.0971.4498.4
2.773.0510010.151.1358.3
2.572.7799.910.2260.917.8
2.422.5799.710.2790.8326.1
2.32.4297.410.3210.834.4
2.22.388.310.3440.9363
2.112.256.910.3830.7562.1
2.042.1122.910.4360.841.6
ReflectionResolution: 2.04→50 Å / Num. obs: 15739 / % possible obs: 86.5 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.083 / Χ2: 1.311 / Net I/σ(I): 10.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.04-2.111.60.4364160.84122.9
2.11-2.22.10.38310360.756156.9
2.2-2.330.34415980.936188.3
2.3-2.424.40.32117600.83197.4
2.42-2.576.10.27918240.832199.7
2.57-2.777.80.22618040.91199.9
2.77-3.058.30.1518221.1351100
3.05-3.498.40.09718201.4491100
3.49-4.398.30.06518292.0771100
4.39-508.20.04618301.655199.5

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACT3data extraction
CBASSdata collection
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.04→20 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.938 / SU B: 8.077 / SU ML: 0.098 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.168 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The Friedel pairs were used in phasing. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.215 436 4.8 %RANDOM
Rwork0.165 ---
obs0.168 9087 89.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 38.829 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20.03 Å20 Å2
2--0.06 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.04→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms955 0 1 57 1013
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.022971
X-RAY DIFFRACTIONr_angle_refined_deg1.6611.9851314
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.495121
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.7726.44445
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.34215193
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.578154
X-RAY DIFFRACTIONr_chiral_restr0.1140.2161
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02701
X-RAY DIFFRACTIONr_nbd_refined0.2120.2468
X-RAY DIFFRACTIONr_nbtor_refined0.310.2691
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1130.251
X-RAY DIFFRACTIONr_metal_ion_refined0.1530.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2580.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3860.211
X-RAY DIFFRACTIONr_mcbond_it1.5551.5600
X-RAY DIFFRACTIONr_mcangle_it5.50420981
X-RAY DIFFRACTIONr_scbond_it11.58720374
X-RAY DIFFRACTIONr_scangle_it6.4464.5332
LS refinement shellResolution: 2.04→2.09 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.215 8 -
Rwork0.216 207 -
all-215 -
obs--29.99 %
Refinement TLS params.Method: refined / Origin x: -4.5335 Å / Origin y: -26.7844 Å / Origin z: 4.5925 Å
111213212223313233
T-0.0936 Å20.0234 Å20.0116 Å2--0.0413 Å20.0403 Å2---0.0959 Å2
L3.7113 °2-1.2841 °20.9747 °2-2.4338 °2-0.2646 °2--3.4012 °2
S0.0061 Å °0.1894 Å °0.2113 Å °-0.0191 Å °-0.0257 Å °0.0816 Å °-0.2026 Å °-0.1888 Å °0.0196 Å °

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