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- PDB-5uxv: Crystal Structure of Anti-anti-sigma factor PhyR I40V/S51C mutant... -

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Basic information

Entry
Database: PDB / ID: 5uxv
TitleCrystal Structure of Anti-anti-sigma factor PhyR I40V/S51C mutant from Bartonella quintana
ComponentsSensory transduction regulatory protein
KeywordsSIGNALING PROTEIN / Bartonella quintana / anti-anti-sigma factor / sensory transduction regulation / two-component response regulation / alphaproteobacteria / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


sigma factor activity / phosphorelay signal transduction system / DNA-templated transcription initiation / DNA binding
Similarity search - Function
Signal transduction response regulator PhyR-like, alphaproteobacteria / PhyR, sigma-like (SL) domain / RNA polymerase sigma factor 70, region 4 type 2 / Sigma-70, region 4 / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / RNA polymerase sigma factor, region 3/4-like / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. ...Signal transduction response regulator PhyR-like, alphaproteobacteria / PhyR, sigma-like (SL) domain / RNA polymerase sigma factor 70, region 4 type 2 / Sigma-70, region 4 / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / RNA polymerase sigma factor, region 3/4-like / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Sensory transduction regulatory protein / Sensory transduction regulatory protein, Anti-anti-sigma factor PhyR
Similarity search - Component
Biological speciesBartonella quintana (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of Anti-anti-sigma factor PhyR I40V/S51C mutant from Bartonella quintana
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Dranow, D.M. / Fairman, J.W. / Lorimer, D. / Edwards, T.E.
History
DepositionFeb 23, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 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: Sensory transduction regulatory protein
B: Sensory transduction regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4304
Polymers59,3062
Non-polymers1242
Water79344
1
A: Sensory transduction regulatory protein


Theoretical massNumber of molelcules
Total (without water)29,6531
Polymers29,6531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sensory transduction regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7773
Polymers29,6531
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.500, 121.420, 89.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Sensory transduction regulatory protein


Mass: 29653.064 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bartonella quintana (bacteria) / Strain: Toulouse / Gene: BQ10980 / Plasmid: BAQUA.17156.A.DG11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3LUV4, UniProt: A0A0M3KKV8*PLUS
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.7 Å3/Da / Density % sol: 54.49 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: SYNERGY1(E12): 7.425% MPD, 0.223M AMMONIUM CITRATE/ CITRIC ACID, PH=5.5 , CRYO PROTECTED WITH 20% EG; BAQUA.17156.A.DG11.PD00341 AT 19.88 MG/ML, TRAY 257812H11
PH range: 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 12, 2014 / Details: BERYLLIUM LENSES
RadiationMonochromator: DIAMOND [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 20022 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 32.97 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.61
Reflection shellResolution: 2.6→2.67 Å / Redundancy: 5 % / Rmerge(I) obs: 0.502 / Mean I/σ(I) obs: 3.24 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIXdev_2666refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
XSCALEdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QIC

4qic


Resolution: 2.6→49.175 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.46
RfactorNum. reflection% reflection
Rfree0.2372 918 4.59 %
Rwork0.194 --
obs0.1961 20018 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→49.175 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3683 0 8 44 3735
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023775
X-RAY DIFFRACTIONf_angle_d0.4975136
X-RAY DIFFRACTIONf_dihedral_angle_d13.672309
X-RAY DIFFRACTIONf_chiral_restr0.039610
X-RAY DIFFRACTIONf_plane_restr0.003667
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.73710.2988990.24942751X-RAY DIFFRACTION100
2.7371-2.90860.31151190.25152715X-RAY DIFFRACTION100
2.9086-3.13310.27651640.23992656X-RAY DIFFRACTION100
3.1331-3.44830.22371460.20362715X-RAY DIFFRACTION100
3.4483-3.94710.22181300.18962712X-RAY DIFFRACTION100
3.9471-4.97220.1777980.15682804X-RAY DIFFRACTION100
4.9722-49.18350.24271620.1682747X-RAY DIFFRACTION97
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)
13.9551-0.26821.71321.1071.22232.4366-0.00090.1878-0.22060.02080.0338-0.1368-0.11920.2385-0.03780.174-0.02260.01240.23520.03010.231911.5434-24.92662.0501
22.5918-0.37480.51192.558-0.14993.41050.00020.405-0.8694-0.0353-0.0897-0.59590.25880.28680.13360.2478-0.08990.00560.4669-0.09080.48625.5257-35.1913-5.108
31.2717-0.3327-0.73992.4562-0.98232.8648-0.11560.6621-0.8958-0.54550.1038-0.9490.2180.58030.05780.3488-0.04130.12590.6845-0.19120.65637.986-36.8813-13.1209
45.9876-3.9682-1.02939.57851.4982.7732-0.0320.15860.0277-0.0642-0.05140.06350.1216-0.30910.08050.2638-0.0334-0.05940.1972-0.00820.1113-16.9011-31.9402-6.5021
53.5418-3.07310.0526.99951.2942.73410.25150.81460.1521-0.8042-0.1140.26570.0549-0.426-0.11120.3785-0.024-0.05860.41060.06590.2246-17.2631-25.7274-14.0451
64.3871-2.3457-1.83983.5706-0.43661.7644-0.0011-0.2051-0.29250.36390.11650.56420.1084-0.2354-0.11480.1835-0.0386-0.03990.3325-0.01490.2541-24.3428-29.5332-2.4735
74.32070.96150.7623.66261.2874.15770.0627-0.16580.22420.0070.04230.2318-0.182-0.2001-0.10330.1840.00770.00180.26450.02250.2408-11.8131-23.9851.8711
87.80890.2643-0.62593.0373.0115.41630.02630.0342-1.247-0.1849-0.0536-0.66950.50120.46060.0770.1731-0.021-0.02540.2808-0.05140.4657-6.9504-37.1903-3.9392
91.014-0.24810.45213.43260.80061.02-0.0290.1272-0.02390.2623-0.0264-0.07810.174-0.10340.05570.2917-0.07810.03370.297-0.03240.19128.7418-2.5259-16.4972
103.35420.92521.24416.051.49975.3767-0.07570.306-0.0129-0.2343-0.12190.3315-0.0206-0.25150.15030.3164-0.0476-0.02820.3201-0.06290.287225.04877.3151-22.3258
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 64 )
2X-RAY DIFFRACTION2chain 'A' and (resid 65 through 108 )
3X-RAY DIFFRACTION3chain 'A' and (resid 109 through 135 )
4X-RAY DIFFRACTION4chain 'A' and (resid 136 through 148 )
5X-RAY DIFFRACTION5chain 'A' and (resid 149 through 161 )
6X-RAY DIFFRACTION6chain 'A' and (resid 162 through 183 )
7X-RAY DIFFRACTION7chain 'A' and (resid 184 through 242 )
8X-RAY DIFFRACTION8chain 'A' and (resid 243 through 262 )
9X-RAY DIFFRACTION9chain 'B' and (resid 2 through 183 )
10X-RAY DIFFRACTION10chain 'B' and (resid 184 through 260 )

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