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- PDB-6eb7: YycF homologue (SP1227) Receiver Domain Activated by BeF3 -

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Basic information

Entry
Database: PDB / ID: 6eb7
TitleYycF homologue (SP1227) Receiver Domain Activated by BeF3
ComponentsDNA-binding response regulator
KeywordsSIGNALING PROTEIN / BeF3 Activated / YycF Homologue / Response Regulator
Function / homology
Function and homology information


phosphorelay signal transduction system / cis-regulatory region sequence-specific DNA binding / fatty acid biosynthetic process / negative regulation of DNA-templated transcription / membrane / 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 ...: / 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 / Response regulator / Winged helix-like DNA-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BERYLLIUM TRIFLUORIDE ION / : / Transcriptional regulatory protein WalR
Similarity search - Component
Biological speciesStreptococcus pneumoniae serotype 4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.58 Å
AuthorsRiboldi-Tunnicliffe, A. / Issacs, N.W.
CitationJournal: To Be Published
Title: YycF homologue (SP1227) Receiver Domain Activated by BeF3
Authors: Riboldi-Tunnicliffe, A.
History
DepositionAug 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1May 4, 2022Group: Advisory / Database references / Category: database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)13,3753
Polymers13,2541
Non-polymers1212
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.563, 93.324, 37.456
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-372-

HOH

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Components

#1: Protein DNA-binding response regulator


Mass: 13254.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4) (bacteria)
Strain: ATCC BAA-334 / TIGR4 / Gene: SP_1227 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H2UQ68
#2: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.46 Å3/Da / Density % sol: 49.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 36% v/v PEG 300, 5% w/v PEG 1,000 100 mM Sodium Acetate pH 5.5
PH range: 6.3 - 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Apr 6, 2001
RadiationMonochromator: Silicon Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.58→29.21 Å / Num. obs: 17717 / % possible obs: 96.42 % / Redundancy: 2 % / Biso Wilson estimate: 20.89 Å2 / CC1/2: 0.995 / Rpim(I) all: 0.06079 / Net I/σ(I): 11.38
Reflection shellResolution: 1.58→1.636 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1.09 / Num. unique obs: 1742 / CC1/2: 0.665 / Rpim(I) all: 0.6138 / % possible all: 95.65

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.45 Å29.21 Å
Translation4.45 Å29.21 Å

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Processing

Software
NameVersionClassificationNB
PHENIX1.13_2998refinement
XDSdata reduction
Aimlessdata scaling
PHASER2.8.1phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.58→29.21 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2155 911 5.15 %
Rwork0.1949 16788 -
obs0.196 17699 96.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86 Å2 / Biso mean: 30.9256 Å2 / Biso min: 14.07 Å2
Refinement stepCycle: final / Resolution: 1.58→29.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms929 0 5 98 1032
Biso mean--25.15 43.05 -
Num. residues----116
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 (%)
1.58-1.66330.38851390.37472349248897
1.6633-1.76750.33191280.32322390251897
1.7675-1.9040.28561440.2692378252298
1.904-2.09550.24911300.20672406253698
2.0955-2.39860.17821280.17142433256198
2.3986-3.02150.19751230.17662419254297
3.0215-29.21460.17721190.16312413253292
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)
13.6028-2.10350.71575.0135-0.49063.42060.27940.571-0.2057-0.15960.0127-0.2742-0.09460.2012-0.31990.27550.03610.00880.2815-0.03080.134260.307563.56164.6232
25.0246-0.24273.51157.1503-1.13612.8662-0.05290.2870.3627-0.2846-0.0645-0.6939-0.67310.2824-0.02930.34250.02150.09330.2981-0.00060.314966.795667.2250.1495
37.64370.9616-1.22852.5237-1.93521.51550.17980.6782-1.2268-0.69930.3464-0.6981.04390.0304-0.38960.59450.0774-0.02550.3802-0.0690.295460.589364.4806-7.6609
42.4598-1.152-0.54592.4536-0.92951.6347-0.0297-0.10220.3080.0682-0.03040.0834-0.07430.01910.05440.36580.0483-0.00030.2497-0.0180.188857.723666.33898.2508
53.4733-1.85844.36037.65790.29997.68190.1110.19390.10060.38720.14960.6899-0.4816-0.2231-0.11010.20520.07280.02320.3388-0.02620.292150.504365.259310.137
67.66442.90863.33122.0032-1.70732.42830.05890.02330.2878-0.14290.07260.92930.317-0.3032-0.37460.3020.06650.00550.26350.00620.118551.309560.24334.2101
70.90471.38711.28462.46392.31112.1993-0.1073-0.29750.091.08740.2555-0.61370.15570.1780.00260.43930.0862-0.07030.3093-0.04020.18464.312359.000513.9613
84.62654.0984-4.09084.1486-4.39254.76660.1385-0.8711-0.35591.0915-0.2840.0030.90560.2499-0.10370.57570.03760.06640.33260.00450.174856.060154.857616.491
95.28791.07160.24892.44940.72321.0934-0.0012-0.14070.04540.63840.06450.23180.0818-0.0907-0.04830.30710.01990.03550.2720.00810.149557.539253.60748.9756
102.93333.01671.65683.27571.09363.3472-0.061-0.0747-0.33240.73870.1431-0.69970.23770.1935-0.14280.50040.0312-0.09010.2891-0.010.206567.364345.439510.8418
114.3417-0.7071-0.45573.77582.044.66930.06530.02890.1728-0.21210.1172-0.2427-0.2130.0587-0.16430.2780.02290.00050.2213-0.02530.140364.083552.88630.2476
124.08931.52911.82367.18182.50285.45030.09960.66290.0737-0.1704-0.29760.63280.2052-0.52210.14220.27310.042-0.13610.3312-0.03120.232952.595351.4909-4.5054
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 2:10)A2 - 10
2X-RAY DIFFRACTION2(chain A and resid 11:19)A11 - 19
3X-RAY DIFFRACTION3(chain A and resid 20:24)A20 - 24
4X-RAY DIFFRACTION4(chain A and resid 25:39)A25 - 39
5X-RAY DIFFRACTION5(chain A and resid 40:44)A40 - 44
6X-RAY DIFFRACTION6(chain A and resid 45:49)A45 - 49
7X-RAY DIFFRACTION7(chain A and resid 50:61)A50 - 61
8X-RAY DIFFRACTION8(chain A and resid 62:67)A62 - 67
9X-RAY DIFFRACTION9(chain A and resid 68:81)A68 - 81
10X-RAY DIFFRACTION10(chain A and resid 82:91)A82 - 91
11X-RAY DIFFRACTION11(chain A and resid 92:112)A92 - 112
12X-RAY DIFFRACTION12(chain A and resid 113:118)A113 - 118

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