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- PDB-2zwm: Crystal structure of YycF receiver domain from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 2zwm
TitleCrystal structure of YycF receiver domain from Bacillus subtilis
ComponentsTranscriptional regulatory protein yycF
KeywordsTRANSCRIPTION / two-component system / response regulator / dimerization domain / phosphorylation site / Cytoplasm / DNA-binding / Phosphoprotein / Transcription regulation / Two-component regulatory system
Function / homology
Function and homology information


phosphorelay response regulator activity / protein-DNA complex / transcription cis-regulatory region binding / regulation of DNA-templated transcription / cytosol
Similarity search - Function
: / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / OmpR/PhoB-type DNA-binding domain profile. / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain ...: / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / OmpR/PhoB-type DNA-binding domain profile. / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / 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
Transcriptional regulatory protein WalR
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsDoi, A. / Okajima, T. / Utsumi, R.
CitationJournal: To be Published
Title: Novel Antibiotics Target Protein of Gram-positive Pathogens: X-ray Crystal Structures and Search of Potential Drug-Binding sites
Authors: Doi, A. / Okajima, T. / Gotoh, Y. / Tanizawa, K. / Utsumi, R.
History
DepositionDec 16, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / 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 / _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: Transcriptional regulatory protein yycF
B: Transcriptional regulatory protein yycF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5316
Polymers30,1472
Non-polymers3844
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-53 kcal/mol
Surface area10940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.824, 58.824, 78.247
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Transcriptional regulatory protein yycF / Response regulator YycF


Mass: 15073.393 Da / Num. of mol.: 2 / Fragment: N-terminal receiver domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: yycF / Plasmid: pET-21a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P37478
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.59 Å3/Da / Density % sol: 52.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2M Potassium sodium tartrate tetrahydrate, 0.1M tri-Sodium citrate dihydrate, 2.0M Ammonium sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Mar 17, 2007
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.04→25.47 Å / Num. all: 19218 / Num. obs: 19194 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 5.6 % / Biso Wilson estimate: 37 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 15.6
Reflection shellResolution: 2.04→2.15 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.417 / Mean I/σ(I) obs: 3.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2A9R

2a9r


Resolution: 2.04→25.47 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.945 / SU B: 8.353 / SU ML: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.73 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22982 935 4.9 %RANDOM
Rwork0.19362 ---
all0.1948 19190 --
obs0.19543 19190 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.533 Å2
Baniso -1Baniso -2Baniso -3
1-1.33 Å20.66 Å20 Å2
2--1.33 Å20 Å2
3----1.99 Å2
Refinement stepCycle: LAST / Resolution: 2.04→25.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1922 0 20 63 2005
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221962
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8862.022646
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.715238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.04325.43592
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.65115394
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.671514
X-RAY DIFFRACTIONr_chiral_restr0.1280.2306
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021426
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2250.2907
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.21332
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.299
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2540.233
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0710.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4821.51200
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.3821952
X-RAY DIFFRACTIONr_scbond_it3.8133762
X-RAY DIFFRACTIONr_scangle_it6.3134.5694
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.04→2.093 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 77 -
Rwork0.256 1319 -
obs-1319 100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.20670.1644-0.00420.13750.03740.2469-0.05120.0231-0.0136-0.05350.0418-0.0058-0.01060.01630.00950.1014-0.01240.00360.0868-0.00170.0522-8.271-11.058-2.5
20.34450.14040.10.06010.01890.19470.0157-0.085-0.0145-0.0101-0.0195-0.00980.0081-0.01910.00370.08080.00110.00070.10840.00450.0543-15.709-15.35921.312
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 120
2X-RAY DIFFRACTION2B1 - 120

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