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- PDB-5i4c: Crystal structure of non-phosphorylated receiver domain of the st... -

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Basic information

Entry
Database: PDB / ID: 5i4c
TitleCrystal structure of non-phosphorylated receiver domain of the stress response regulator RcsB from Escherichia coli
ComponentsTranscriptional regulatory protein RcsB
KeywordsGENE REGULATION / Rcs phosphorelay / DNA-binding / transcriptional regulator / rprA / Structural Genomics / CSGID / Center for Structural Genomics of Infectious Diseases / HYDROLASE
Function / homology
Function and homology information


regulation of capsule organization / regulation of carbohydrate catabolic process / single-species biofilm formation on inanimate substrate / positive regulation of cell projection organization / cellular stress response to acidic pH / regulation of bacterial-type flagellum-dependent cell motility / DNA-binding transcription repressor activity / DNA-binding transcription activator activity / phosphorelay signal transduction system / transcription regulator complex ...regulation of capsule organization / regulation of carbohydrate catabolic process / single-species biofilm formation on inanimate substrate / positive regulation of cell projection organization / cellular stress response to acidic pH / regulation of bacterial-type flagellum-dependent cell motility / DNA-binding transcription repressor activity / DNA-binding transcription activator activity / phosphorelay signal transduction system / transcription regulator complex / response to antibiotic / negative regulation of DNA-templated transcription / DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / DNA binding / identical protein binding / cytosol
Similarity search - Function
Transcriptional regulatory protein RcsB / LuxR-type HTH domain signature. / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain ...Transcriptional regulatory protein RcsB / LuxR-type HTH domain signature. / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / 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
Transcriptional regulatory protein RcsB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsFilippova, E.V. / Wawrzak, Z. / Minasov, G. / Ruan, J. / Pshenychnyi, S. / Wolfe, A.J. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Protein Sci. / Year: 2016
Title: Crystal structure of nonphosphorylated receiver domain of the stress response regulator RcsB from Escherichia coli.
Authors: Filippova, E.V. / Wawrzak, Z. / Ruan, J. / Pshenychnyi, S. / Schultz, R.M. / Wolfe, A.J. / Anderson, W.F.
History
DepositionFeb 11, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2016Group: Database references
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Database references / Category: citation / pdbx_struct_assembly_auth_evidence / Item: _citation.journal_id_CSD
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulatory protein RcsB


Theoretical massNumber of molelcules
Total (without water)16,0381
Polymers16,0381
Non-polymers00
Water1,45981
1
A: Transcriptional regulatory protein RcsB

A: Transcriptional regulatory protein RcsB


Theoretical massNumber of molelcules
Total (without water)32,0752
Polymers32,0752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area1060 Å2
ΔGint-11 kcal/mol
Surface area12540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.197, 61.197, 65.226
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-240-

HOH

DetailsSEC-MALS analysis also shows that protein can exist in dimeric state

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Components

#1: Protein Transcriptional regulatory protein RcsB / Capsular synthesis regulator component B


Mass: 16037.635 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: rcsB, b2217, JW2205 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 magic / References: UniProt: P0DMC7
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.2 Å3/Da / Density % sol: 44.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 3.5 M Sodium Formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 25, 2014 / Details: beryllium lenses
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 9939 / % possible obs: 100 % / Redundancy: 8.6 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 20.1
Reflection shellResolution: 2→2.03 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data scaling
PHENIXmodel building
BALBESphasing
HKL-2000data reduction
RefinementResolution: 2→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.925 / SU B: 8.573 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.165 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23775 497 5 %RANDOM
Rwork0.17262 ---
obs0.17589 9421 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 37.859 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20.12 Å20 Å2
2--0.24 Å2-0 Å2
3----0.79 Å2
Refinement stepCycle: 1 / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1011 0 0 81 1092
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191038
X-RAY DIFFRACTIONr_bond_other_d0.0020.021047
X-RAY DIFFRACTIONr_angle_refined_deg2.0161.9911413
X-RAY DIFFRACTIONr_angle_other_deg1.07432420
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9175132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.34726.58541
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.27115188
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.203152
X-RAY DIFFRACTIONr_chiral_restr0.1190.2171
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211154
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02202
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7522.669528
X-RAY DIFFRACTIONr_mcbond_other1.7532.666527
X-RAY DIFFRACTIONr_mcangle_it2.6013.99660
X-RAY DIFFRACTIONr_mcangle_other2.5993.993661
X-RAY DIFFRACTIONr_scbond_it2.6243.005510
X-RAY DIFFRACTIONr_scbond_other2.6022.998508
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0664.389753
X-RAY DIFFRACTIONr_long_range_B_refined6.57522.7881192
X-RAY DIFFRACTIONr_long_range_B_other6.49422.3211166
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.999→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 28 -
Rwork0.24 687 -
obs--98.08 %
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)
10.4268-0.4845-0.46922.14140.0425.17440.08340.0604-0.0845-0.1384-0.13780.10450.0293-0.16770.05450.02490.0164-0.02440.0695-0.00220.07056.775721.97947.5334
21.3895-0.652-0.50372.36710.96652.87690.0597-0.0471-0.1011-0.0641-0.2290.27420.0976-0.09420.16930.0184-0.0054-0.01620.0611-0.00210.05593.348926.57113.2899
33.38570.5847-1.21883.2483-2.49337.8891-0.1244-0.14170.04980.1504-0.0922-0.219-0.46580.17430.21660.0452-0.0117-0.01110.0206-0.00790.02899.161238.795916.4631
43.804-1.2235-3.6353.76261.43933.49870.084-0.44120.1174-0.09770.053-0.276-0.10.3975-0.1370.04140.0197-0.00570.159-0.01520.03914.301530.965317.7176
513.41340.5651-5.27687.0485-1.24844.7601-0.55050.71920.14940.23520.7132-0.11310.0095-0.0008-0.16280.096-0.0679-0.02840.1978-0.00720.024520.194432.167122.097
63.54260.704-0.93141.1905-0.51964.4099-0.1435-0.2001-0.362-0.0750.1031-0.14760.25810.0610.04040.06190.05490.01730.10670.0280.057616.408519.866316.5245
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 24
2X-RAY DIFFRACTION2A25 - 58
3X-RAY DIFFRACTION3A59 - 75
4X-RAY DIFFRACTION4A76 - 94
5X-RAY DIFFRACTION5A95 - 102
6X-RAY DIFFRACTION6A103 - 132

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