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- PDB-4cxf: Structure of CnrH in complex with the cytosolic domain of CnrY -

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Basic information

Entry
Database: PDB / ID: 4cxf
TitleStructure of CnrH in complex with the cytosolic domain of CnrY
Components
  • CNRY
  • RNA POLYMERASE SIGMA FACTOR CNRH
KeywordsTRANSCRIPTION / ECF-TYPE SIGMA / ANTISIGMA
Function / homology
Function and homology information


sigma factor activity / DNA-templated transcription initiation / membrane => GO:0016020 / DNA-binding transcription factor activity / DNA binding / plasma membrane
Similarity search - Function
Anti-sigma factor CnrY / Anti-sigma factor CnrY / RNA polymerase sigma factor 70, region 4 type 2 / Sigma-70, region 4 / RNA polymerase sigma factor 70, ECF, conserved site / Sigma-70 factors ECF subfamily signature. / RNA polymerase sigma-70 like / RNA polymerase sigma factor, region 2, helix turn helix motif / Rna Polymerase Sigma Factor; Chain: A / RNA polymerase sigma-70 region 2 ...Anti-sigma factor CnrY / Anti-sigma factor CnrY / RNA polymerase sigma factor 70, region 4 type 2 / Sigma-70, region 4 / RNA polymerase sigma factor 70, ECF, conserved site / Sigma-70 factors ECF subfamily signature. / RNA polymerase sigma-70 like / RNA polymerase sigma factor, region 2, helix turn helix motif / Rna Polymerase Sigma Factor; Chain: A / RNA polymerase sigma-70 region 2 / RNA polymerase sigma-70 like domain / Sigma-70 region 2 / RNA polymerase sigma factor, region 2 / RNA polymerase sigma factor, region 3/4-like / 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
RNA polymerase sigma factor CnrH / Nickel and cobalt resistance protein CnrY
Similarity search - Component
Biological speciesCUPRIAVIDUS METALLIDURANS CH34 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsMaillard, A.P. / Girard, E. / Ziani, W. / Petit-Hartlein, I. / Kahn, R. / Coves, J.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: The Crystal Structure of the Anti-Sigma Factor Cnry in Complex with the Sigma Factor Cnrh Shows a New Structural Class of Anti- Sigma Factors Targeting Extracytoplasmic-Function Sigma Factors.
Authors: Maillard, A.P. / Girard, E. / Ziani, W. / Petit-Hartlein, I. / Kahn, R. / Coves, J.
History
DepositionApr 7, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 4, 2014Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: RNA POLYMERASE SIGMA FACTOR CNRH
B: CNRY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2297
Polymers30,8092
Non-polymers4205
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-68.2 kcal/mol
Surface area9590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.010, 79.122, 80.537
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-2008-

HOH

21A-2027-

HOH

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Components

#1: Protein RNA POLYMERASE SIGMA FACTOR CNRH / CNRH


Mass: 20648.334 Da / Num. of mol.: 1 / Fragment: SIGMA2 AND SIGMA4 DOMAINS, RESIDUES 1-191
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CUPRIAVIDUS METALLIDURANS CH34 (bacteria)
Plasmid: PET-DUET-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: P37978
#2: Protein CNRY


Mass: 10160.793 Da / Num. of mol.: 1 / Fragment: CYTOSOLIC DOMAIN, RESIDUES 1-95
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CUPRIAVIDUS METALLIDURANS CH34 (bacteria)
Plasmid: PET-DUET-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: P56621
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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 % sol: 25 % / Description: NONE
Crystal growpH: 7.5
Details: 2.0 TO 2.2 M AMMONIUM SULFATE, 100 MM HEPES PH 7.5 AND 2 % PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Details: PT COATED SI MIRROR IN A
RadiationMonochromator: SILICON 111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.75→39.56 Å / Num. obs: 19854 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 20.4
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.5 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.75→39.561 Å / SU ML: 0.25 / σ(F): 1.34 / Phase error: 18.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2009 995 5 %
Rwork0.174 --
obs0.1754 19830 98.9 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.101 Å2 / ksol: 0.37 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.6529 Å20 Å20 Å2
2---4.4968 Å20 Å2
3---8.1497 Å2
Refinement stepCycle: LAST / Resolution: 1.75→39.561 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1397 0 21 144 1562
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071508
X-RAY DIFFRACTIONf_angle_d1.0712054
X-RAY DIFFRACTIONf_dihedral_angle_d13.72550
X-RAY DIFFRACTIONf_chiral_restr0.077233
X-RAY DIFFRACTIONf_plane_restr0.005272
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7501-1.84230.32981420.29282703X-RAY DIFFRACTION100
1.8423-1.95780.25271400.21232679X-RAY DIFFRACTION100
1.9578-2.10890.21561420.16752678X-RAY DIFFRACTION100
2.1089-2.32110.16511410.15612669X-RAY DIFFRACTION100
2.3211-2.65690.1881470.15482703X-RAY DIFFRACTION99
2.6569-3.34720.22171380.17012694X-RAY DIFFRACTION98
3.3472-39.57110.18121450.17082709X-RAY DIFFRACTION95
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)
11.55771.0239-0.53242.9464-1.09581.5369-0.12970.0436-0.0886-0.26270.08590.04320.09350.02150.0310.18180.00330.0170.14170.00920.111417.768125.797747.5574
23.49030.8794-0.31963.4247-0.17171.5418-0.0183-0.6373-0.08350.1107-0.0208-0.0612-0.05590.0584-0.0040.14690.02140.01190.22760.02930.129220.238826.494856.9929
30.27060.86370.79177.33972.91197.2415-0.48480.94970.2841-1.30830.35080.74170.4134-0.80580.26810.4783-0.18780.01990.540.09450.4543.6718.538252.3557
45.10220.29781.40863.9181-0.83336.7455-0.0557-0.1936-0.6817-0.21830.34260.32010.6233-0.2948-0.0560.2477-0.04940.06940.17260.09730.336610.18734.652556.5962
52.5020.6934-0.10172.70450.21851.3812-0.0812-0.0247-0.0948-0.01850.0074-0.28150.00650.04270.08090.14540.00860.02130.20110.0790.225523.724714.314860.9758
65.41543.78860.92263.84561.60912.31950.03630.0568-0.2675-0.0651-0.0464-0.91420.2174-0.02960.11780.21240.01810.0640.22180.11460.337219.16191.46263.5134
74.5341-2.25011.70527.7091-2.61884.8928-0.01260.4426-0.4034-1.1665-0.4431-0.20540.44160.66170.41990.5077-0.050.170.27810.00040.287418.29474.646948.6065
81.38741.0561.54672.5075-0.93924.3531-0.02830.15090.0966-0.51980.20670.4857-0.1227-0.29110.15250.81670.1199-0.3311.11370.18990.565111.90629.164440.7048
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 5:61)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 62:88)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 89:126)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 127:139)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 140:170)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 171:189)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 2:21)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 22:30)

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