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- PDB-3f7a: Structure of Orthorhombic crystal form of Pseudomonas aeruginosa RssB -

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Basic information

Entry
Database: PDB / ID: 3f7a
TitleStructure of Orthorhombic crystal form of Pseudomonas aeruginosa RssB
ComponentsProbable two-component response regulator
KeywordsSIGNALING PROTEIN / ADAPTOR PHOSPHATASE / UNKNOWN FUNCTION
Function / homology
Function and homology information


phosphorelay response regulator activity / protein-DNA complex / transcription cis-regulatory region binding / regulation of DNA-templated transcription / metal ion binding / cytosol
Similarity search - Function
: / Stage II sporulation protein E (SpoIIE) / Sigma factor PP2C-like phosphatases / PPM-type phosphatase-like domain / PPM-type phosphatase-like domain superfamily / Transcriptional regulatory protein WalR-like / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily
Similarity search - Domain/homology
Probable two-component response regulator
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 4.308 Å
Authorslevchenko, I. / Grant, R.A. / Sauer, R.T. / Baker, T.A.
CitationJournal: To be Published
Title: The structure of RSSB, a CLPX adaptor protein that regulates sigma S
Authors: Levchenko, I. / Grant, R.A. / Sauer, R.T. / Baker, T.A.
History
DepositionNov 7, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Dec 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable two-component response regulator
B: Probable two-component response regulator


Theoretical massNumber of molelcules
Total (without water)87,6222
Polymers87,6222
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-28 kcal/mol
Surface area38080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.873, 178.970, 57.067
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Probable two-component response regulator


Mass: 43811.020 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA2798 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I045

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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: 3.52 Å3/Da / Density % sol: 65.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion / Details: VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97932 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 5, 2007 / Details: crystal monochromometer
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 4.3→50 Å / Num. obs: 8886 / % possible obs: 99.8 % / Redundancy: 18.5 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 39.667
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
4.3-4.4516.70.49299.2
4.45-4.6317.60.29799.8
4.63-4.8418.30.2799.7
4.84-5.118.80.245100
5.1-5.4219.30.283100
5.42-5.8319.50.227100
5.83-6.4219.50.182100
6.42-7.3519.20.121100
7.35-9.2518.20.077100
9.25-5017.60.05699.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
RefinementResolution: 4.308→39.307 Å / SU ML: 0.94 / σ(F): 1.95 / Phase error: 40.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3417 741 4.62 %
Rwork0.296 --
obs0.298 16037 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 196.642 Å2 / ksol: 0.305 e/Å3
Refinement stepCycle: LAST / Resolution: 4.308→39.307 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5617 0 0 0 5617
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025693
X-RAY DIFFRACTIONf_angle_d0.5567726
X-RAY DIFFRACTIONf_dihedral_angle_d9.7912037
X-RAY DIFFRACTIONf_chiral_restr0.036927
X-RAY DIFFRACTIONf_plane_restr0.0031009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.308-4.63970.41281430.35052997X-RAY DIFFRACTION98
4.6397-5.10580.32641620.31263066X-RAY DIFFRACTION99
5.1058-5.84250.40851560.31643065X-RAY DIFFRACTION100
5.8425-7.3530.35651320.30493078X-RAY DIFFRACTION100
7.353-39.30880.28841480.23743090X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
18.98710.26150.69187.963-0.124410.17931.4146-0.1919-0.9337-0.3842-0.3391.0592-1.1414-1.2638-0.0012.83420.04990.04771.9260.04922.9753-38.04330.5256-18.8691
22.0971-0.5013.67011.364-3.88-0.45330.5692-0.672-1.5555-0.48590.0951-0.1020.2871-0.07240.00123.14060.1293-0.25642.544-0.2663.3832-20.135623.0471-6.3942
30.5857-1.13270.28352.7099-0.8597-2.16422.52480.2151-0.01640.4886-2.2728-2.1949-1.16972.15030.00324.02970.02490.33673.15041.31813.878617.631827.658611.9424
46.7212-1.5388-5.44552.96573.687512.1503-0.5163-0.15750.226-0.54270.7019-1.0806-0.11251.14610.00023.2367-0.16580.00792.02930.25893.630135.280412.883116.4086
510.24997.1739-7.52828.5685-1.49636.3976-0.18061.7165-0.129-0.7498-0.4373-0.0582-0.58880.17660.00083.4561-0.23080.39552.2443-0.2492.9185-20.030112.0124-34.5744
6-0.7534.85611.6474-3.60592.80563.96-0.20831.0144-0.5322-1.09560.7867-0.66190.36012.58960.00083.6987-0.0482-0.51452.5051-0.12742.9388-9.261921.5092-17.1507
7-0.2687-2.7956-0.6782-0.24151.73540.54461.3426-4.0743-0.9321-0.9963-0.9586-1.3574-0.5736-2.090.00593.8043-1.13170.21773.3468-0.52363.89488.608420.68321.5985
87.924-3.169-4.61577.37582.23036.78590.4402-0.54550.46471.251-0.09960.39591.0123-0.8334-0.00013.6815-0.6210.09852.55190.09712.92214.008637.120637.1595
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1Chain A and resid 5-111
2X-RAY DIFFRACTION2Chain A and resid 112-147
3X-RAY DIFFRACTION3Chain A and resid 148-167
4X-RAY DIFFRACTION4Chain A and resid 168-392
5X-RAY DIFFRACTION5Chain B and resid 5-111
6X-RAY DIFFRACTION6Chain B and resid 112-147
7X-RAY DIFFRACTION7Chain B and resid 148-167
8X-RAY DIFFRACTION8Chain B and resid 168-392

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