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- PDB-2qsj: Crystal structure of a LuxR family DNA-binding response regulator... -

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Basic information

Entry
Database: PDB / ID: 2qsj
TitleCrystal structure of a LuxR family DNA-binding response regulator from Silicibacter pomeroyi
ComponentsDNA-binding response regulator, LuxR family
KeywordsTRANSCRIPTION / STRUCTURAL GENOMICS / DNA BINDING / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC / 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 / Winged helix-like DNA-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA-binding response regulator, LuxR family
Similarity search - Component
Biological speciesSilicibacter pomeroyi DSS-3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsBonanno, J.B. / Freeman, J. / Bain, K.T. / Mendoza, M. / Romero, R. / Smith, D. / Wasserman, S. / 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 a LuxR family DNA-binding response regulator from Silicibacter pomeroyi.
Authors: Bonanno, J.B. / Freeman, J. / Bain, K.T. / Mendoza, M. / Romero, R. / Smith, D. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionJul 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: 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 / Structure summary
Category: audit_author / citation_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details
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
Remark 300 BIOMOLECULE: 1, 2, 3 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY ... BIOMOLECULE: 1, 2, 3 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. AUTHORS STATE THAT THE DIMERIC ASSEMBLY OF THE BIOLOGICAL UNIT OF THIS POLYPEPTIDE IS PROBABLE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA-binding response regulator, LuxR family
B: DNA-binding response regulator, LuxR family


Theoretical massNumber of molelcules
Total (without water)33,1372
Polymers33,1372
Non-polymers00
Water52229
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: DNA-binding response regulator, LuxR family


Theoretical massNumber of molelcules
Total (without water)16,5691
Polymers16,5691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: DNA-binding response regulator, LuxR family


Theoretical massNumber of molelcules
Total (without water)16,5691
Polymers16,5691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.459, 57.459, 111.354
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Detailsprobable dimer

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Components

#1: Protein DNA-binding response regulator, LuxR family


Mass: 16568.732 Da / Num. of mol.: 2 / Fragment: Residues 2-144
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Silicibacter pomeroyi DSS-3 (bacteria) / Species: Silicibacter pomeroyiRuegeria pomeroyi / Strain: DSS-3, DSM 15171 / Gene: SPO2369 / Plasmid: modified pET26 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5LQW4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.77 Å3/Da / Density % sol: 55.65 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 5.5
Details: 100 mM Bis-Tris pH 5.5, 17% PEG 10000, 100 mM Ammonium acetate, VAPOR DIFFUSION, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97958 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 29, 2007
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 2.1→57.459 Å / Num. all: 21057 / Num. obs: 21057 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.6 % / Biso Wilson estimate: 46 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 24.9
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 12.6 % / Rmerge(I) obs: 0.592 / Mean I/σ(I) obs: 4.4 / Num. unique all: 3084 / Rsym value: 0.592 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT3data extraction
MAR345CCDdata collection
MOSFLMdata reduction
SHELXCDphasing
SHELXEmodel building
RefinementResolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.918 / SU B: 5.048 / SU ML: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.187 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1079 5.1 %RANDOM
Rwork0.228 ---
all0.23 21028 --
obs0.23 21028 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 60.255 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å20 Å2
2--0.33 Å20 Å2
3----0.66 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1825 0 0 29 1854
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221847
X-RAY DIFFRACTIONr_angle_refined_deg1.5541.9892504
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1325236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.29424.28677
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.47515309
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5261512
X-RAY DIFFRACTIONr_chiral_restr0.1110.2312
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021350
X-RAY DIFFRACTIONr_nbd_refined0.2190.2793
X-RAY DIFFRACTIONr_nbtor_refined0.3110.21277
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.276
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2840.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1270.24
X-RAY DIFFRACTIONr_mcbond_it1.2411.51239
X-RAY DIFFRACTIONr_mcangle_it2.1321907
X-RAY DIFFRACTIONr_scbond_it2.7613672
X-RAY DIFFRACTIONr_scangle_it4.4434.5597
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 79 -
Rwork0.275 1459 -
all-1538 -
obs-1459 99.94 %

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