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- PDB-4qic: Co-Crystal Structure of Anti-anti-sigma factor PhyR complexed wit... -

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Basic information

Entry
Database: PDB / ID: 4qic
TitleCo-Crystal Structure of Anti-anti-sigma factor PhyR complexed with Anti-sigma factor NepR from Bartonella quintana
Components
  • Anti-sigma factor NepR
  • Sensory transduction regulatory protein, Anti-anti-sigma factor PhyR
KeywordsSIGNALING PROTEIN/DNA BINDING PROTEIN / like domain / are two-component signaling receiver domain / anti-sigma factor domain / sensory tranduction regulation / anti-sigma factor binding / SIGNALING PROTEIN-DNA BINDING PROTEIN complex / 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 transcription factor activity / DNA binding
Similarity search - Function
Anti-sigma factor NepR / Anti-sigma factor NepR / Signal transduction response regulator PhyR-like, alphaproteobacteria / : / : / Sigma2 domain of PhyR / Response regulator PhyR, sigma-like domain / PhyR, sigma-like (SL) domain / RNA polymerase sigma factor 70, region 4 type 2 / Sigma-70, region 4 ...Anti-sigma factor NepR / Anti-sigma factor NepR / Signal transduction response regulator PhyR-like, alphaproteobacteria / : / : / Sigma2 domain of PhyR / Response regulator PhyR, sigma-like domain / 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
Anti-sigma factor NepR / Sensory transduction regulatory protein, Anti-anti-sigma factor PhyR / Anti-sigma factor NepR / Sensory transduction regulatory protein
Similarity search - Component
Biological speciesBartonella quintana (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Co-Crystal Structure of Anti-anti-sigma factor PhyR complexed with Anti-sigma factor NepR from Bartonella quintana
Authors: Dranow, D.M. / Edwards, T.E. / Lorimer, D.
History
DepositionMay 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Sep 20, 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

Downloads & links

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Assembly

Deposited unit
A: Sensory transduction regulatory protein, Anti-anti-sigma factor PhyR
B: Anti-sigma factor NepR
C: Sensory transduction regulatory protein, Anti-anti-sigma factor PhyR
D: Anti-sigma factor NepR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,1567
Polymers80,8584
Non-polymers2983
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14890 Å2
ΔGint-143 kcal/mol
Surface area24480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.800, 86.700, 106.110
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 Sensory transduction regulatory protein, Anti-anti-sigma factor PhyR


Mass: 30978.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bartonella quintana (bacteria) / Strain: Toulouse / Gene: BQ10980 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6G0Z8, UniProt: A0A0M3KKV8*PLUS
#2: Protein Anti-sigma factor NepR


Mass: 9450.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bartonella quintana (bacteria) / Strain: Toulouse / Gene: BQ10970 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6G0Y8, UniProt: A0A0H3LV19*PLUS
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.18 Å3/Da / Density % sol: 43.69 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Morpheus(c8): 12.5% PEG-1000, 12.5% PEG-3350, 12.5% MPD, 0.1M MOPS/ HEPES-Na, 0.03M each sodium nitrate, disodium hydrogen phosphate, ammonium sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 29, 2004 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. all: 45212 / Num. obs: 45189 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 34.274 Å2 / Rmerge(I) obs: 0.075 / Χ2: 0.937 / Net I/σ(I): 16.64
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.05-2.10.5323.31203193278100
2.1-2.160.4334.06199483205100
2.16-2.220.335.3196623157100
2.22-2.290.2786.23187243018100
2.29-2.370.2277.49183402948100
2.37-2.450.1938.57177132842100
2.45-2.540.16410.16173102778100
2.54-2.650.13512.0716588267099.9
2.65-2.760.11613.81157222531100
2.76-2.90.09116.64152882459100
2.9-3.060.07719.45143862326100
3.06-3.240.06223.03136502206100
3.24-3.470.05127.81128862090100
3.47-3.740.04431.3812050196499.9
3.74-4.10.04135.73109371797100
4.1-4.580.0439.0598721635100
4.58-5.290.03739.5187521458100
5.29-6.480.03835.8474071253100
6.48-9.170.03639.785628990100
9.170.04140.76287458497.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.05 Å45.25 Å
Translation2.05 Å45.25 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.6phasing
REFMAC5.8.0071refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4G97

4g97


Resolution: 2.05→19.91 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.2105 / WRfactor Rwork: 0.1801 / FOM work R set: 0.8356 / SU B: 7.943 / SU ML: 0.114 / SU R Cruickshank DPI: 0.177 / SU Rfree: 0.1523 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.177 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2186 2235 5 %RANDOM
Rwork0.1891 ---
obs0.1905 45074 99.83 %-
all-47309 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 87.39 Å2 / Biso mean: 32.407 Å2 / Biso min: 15.67 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å2-0 Å2-0 Å2
2---0.79 Å2-0 Å2
3---1.49 Å2
Refinement stepCycle: LAST / Resolution: 2.05→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4508 0 20 229 4757
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194626
X-RAY DIFFRACTIONr_bond_other_d0.0010.024468
X-RAY DIFFRACTIONr_angle_refined_deg1.4321.9766287
X-RAY DIFFRACTIONr_angle_other_deg0.809310198
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5175589
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.4523.892203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.15315759
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3461534
X-RAY DIFFRACTIONr_chiral_restr0.0810.2749
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215232
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021046
X-RAY DIFFRACTIONr_mcbond_it1.3871.4032353
X-RAY DIFFRACTIONr_mcbond_other1.3881.4032352
X-RAY DIFFRACTIONr_mcangle_it2.4012.0832931
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 170 -
Rwork0.255 3072 -
all-3242 -
obs--99.88 %
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)
10.1761-0.0398-0.32440.58610.19740.6476-0.03-0.03060.01940.08880.0115-0.01740.09570.06630.01850.23430.0150.00110.2808-0.00450.122261.1753.8098.667
20.2676-0.1560.08833.54540.5661.56840.0359-0.09130.05310.1057-0.0039-0.12260.01430.2099-0.0320.23650.03910.05760.1925-0.00480.133168.40830.709-4.501
30.38590.50680.09091.7029-0.34880.68690.00110.0957-0.02490.07-0.035-0.0171-0.00770.0310.03390.23450.01180.01570.3102-0.01470.104469.64340.937-21.495
40.2209-0.0938-0.08240.47020.05610.2730.05120.02240.0492-0.03670.037-0.0073-0.09010.0009-0.08820.238-0.00670.04220.25480.01360.159867.73673.621-9.53
50.43851.0716-0.26134.43231.39832.51060.15840.02710.08040.1560.01810.1533-0.35330.0195-0.17650.2687-0.00040.04720.2594-0.0360.131361.08537.455-14.793
611.3697-7.7733-8.40685.32995.76266.2871-0.145-0.98541.04820.09160.7523-0.7120.19730.8754-0.60730.27310.09080.16980.55390.1410.637469.0116.221-26.893
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 257
2X-RAY DIFFRACTION2B30 - 61
3X-RAY DIFFRACTION3C2 - 114
4X-RAY DIFFRACTION4C115 - 257
5X-RAY DIFFRACTION5D26 - 59
6X-RAY DIFFRACTION6D60 - 64

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