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- PDB-6cqg: YycF Effector Domain Structure without DNA bound -

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Basic information

Entry
Database: PDB / ID: 6cqg
TitleYycF Effector Domain Structure without DNA bound
ComponentsDNA-binding response regulator
KeywordsDNA BINDING PROTEIN / DNA-Binding-Protein / Two-Component-System / Effector-Domain / Winged-helix-turn-helix-DNA-binding domain
Function / homology
Function and homology information


phosphorelay response regulator activity / DNA-binding transcription activator activity / phosphorelay signal transduction system / protein-DNA complex / transcription cis-regulatory region binding / regulation of DNA-templated transcription / DNA binding / cytosol
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 / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. ...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 / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / 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
DNA-binding response regulator / Response regulator
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / MAD / molecular replacement / Resolution: 1.932 Å
AuthorsRiboldi-Tunnicliffe, A. / Gabrielsen, M. / Williamson, R.M. / Panjikar, S.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)QLRK2-2000-00542European Union
CitationJournal: To Be Published
Title: YycF Effector Domain Structure without DNA bound
Authors: Gabrielsen, M. / Williamson, R.M. / Panjikar, S. / Riboldi-Tunnicliffe, A.
History
DepositionMar 15, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.country / _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: DNA-binding response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6662
Polymers11,6011
Non-polymers651
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.630, 46.490, 63.270
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DNA-binding response regulator


Mass: 11601.081 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: yycF, ERS021524_01324
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A0T8EJ76, UniProt: Q8DPL7*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.07 Å3/Da / Density % sol: 40.53 % / Description: Plate like crystal
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6 / Details: 200mM ammonium formate, 20%(w/v) PEG 3350 pH 6.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 26, 2003
RadiationMonochromator: Silicon Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.93→37.46 Å / Num. obs: 7516 / % possible obs: 98 % / Redundancy: 9.1 % / Biso Wilson estimate: 28.1 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.025 / Rrim(I) all: 0.077 / Net I/σ(I): 17
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.93-1.974.50.5714060.7910.2660.63483.3
1.93-37.466.70.047890.9980.0190.05192.3

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Phasing

Phasing
Method
MAD
molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.28data scaling
PHENIX1.13.2998refinement
PDB_EXTRACT3.24data extraction
Auto-Rickshawphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GXQ

1gxq


Resolution: 1.932→31.635 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 22.69
RfactorNum. reflection% reflection
Rfree0.2358 962 12 %
Rwork0.1843 --
obs0.1908 7413 97.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 101.53 Å2 / Biso mean: 35.7643 Å2 / Biso min: 15.82 Å2
Refinement stepCycle: final / Resolution: 1.932→31.635 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms819 0 1 64 884
Biso mean--36.93 38.83 -
Num. residues----98
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9322-2.0340.29871220.232782794989
2.034-2.16140.26721290.2129909103898
2.1614-2.32830.27241460.2051903104998
2.3283-2.56250.25291460.1937912105899
2.5625-2.93310.2521570.2004920107798
2.9331-3.69440.22921180.1776966108499
3.6944-31.63920.2021440.16361014115898
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)
15.11092.53950.2427.094-0.38188.3255-0.20180.30620.5015-0.16570.17940.5766-0.7442-0.74270.10390.27530.0279-0.02150.3653-0.01430.2856-10.34227.874710.4483
25.23540.4089-1.94565.06823.30794.0704-0.10360.28520.4009-0.3626-0.1183-0.4467-0.083-0.25650.21630.3010.0042-0.01740.28560.00280.3092-1.33218.650210.1137
35.63960.30190.75463.4608-2.40195.6048-0.13161.123-0.3312-0.47220.15010.22820.334-0.2450.19530.18250.0329-0.05220.2873-0.01850.2172-9.4927-1.45415.1401
49.117-1.48080.36859.3879-3.19385.6006-0.20040.3275-0.0437-0.13380.41910.29240.5786-0.56720.17170.2197-0.0217-0.0420.2749-0.03860.3045-11.9389-11.07376.0939
51.8489-2.8042-0.49154.55680.77490.13210.07182.2434-1.1148-0.8423-0.1991-0.40291.2511-2.1542-0.43380.6935-0.22520.0441.0521-0.08390.6062-5.5217-13.4714-4.0355
64.3084-0.7911-0.29163.8935-0.08051.51-0.24420.25840.1455-0.23210.1441-0.44080.02770.6506-0.77120.24940.0059-0.01460.2715-0.00880.17260.4863-6.97639.1083
75.1625-0.13583.40274.01910.81663.6382-0.1204-0.84040.42260.96830.1202-0.2672-0.3509-0.16880.09470.3845-0.0165-0.04990.3185-0.04740.2528-1.1628-2.114920.6635
86.8722-0.66440.313.49761.26225.3711-0.0663-0.7995-0.44350.72720.09011.07290.1094-0.51120.15830.35270.01410.0480.33910.00710.2411-9.4769-9.664616.4934
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 133 through 150 )A133 - 150
2X-RAY DIFFRACTION2chain 'A' and (resid 151 through 158 )A151 - 158
3X-RAY DIFFRACTION3chain 'A' and (resid 159 through 171 )A159 - 171
4X-RAY DIFFRACTION4chain 'A' and (resid 172 through 185 )A172 - 185
5X-RAY DIFFRACTION5chain 'A' and (resid 186 through 193 )A186 - 193
6X-RAY DIFFRACTION6chain 'A' and (resid 194 through 208 )A194 - 208
7X-RAY DIFFRACTION7chain 'A' and (resid 209 through 217 )A209 - 217
8X-RAY DIFFRACTION8chain 'A' and (resid 218 through 230 )A218 - 232

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