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- PDB-3es2: Structure of the C-terminal phosphatase domain of P. aeruginonsa RssB -

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Basic information

Entry
Database: PDB / ID: 3es2
TitleStructure of the C-terminal phosphatase domain of P. aeruginonsa 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 domain / Phosphatase 2c; domain 1 / PPM-type phosphatase-like domain / PPM-type phosphatase-like domain superfamily / Transcriptional regulatory protein WalR-like / Response regulator receiver domain / cheY-homologous receiver domain ...: / Stage II sporulation protein E (SpoIIE) / Sigma factor PP2C-like phosphatases / PPM-type phosphatase domain / Phosphatase 2c; domain 1 / 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 / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Probable two-component response regulator
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.95 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
DepositionOct 3, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3Dec 27, 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 / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)56,3042
Polymers56,3042
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-23 kcal/mol
Surface area21540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.211, 70.211, 92.924
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and backbone and resi 149-184
21chain B and backbone and resi 149-184
12chain A and backbone and resi 190-197
22chain B and backbone and resi 190-197
13chain A and backbone and resi 204-235
23chain B and backbone and resi 204-235
14chain A and backbone and resi 249-258
24chain B and backbone and resi 249-258
15chain A and backbone and resi 266-274
25chain B and backbone and resi 266-274
16chain A and backbone and resi 280-293
26chain B and backbone and resi 280-293
17chain A and backbone and resi 301-306
27chain B and backbone and resi 301-306
18chain A and backbone and resi 320-327
28chain B and backbone and resi 320-327
19chain A and backbone and resi 330-334
29chain B and backbone and resi 330-334
110chain A and backbone and resi 348-362
210chain B and backbone and resi 348-362
111chain A and backbone and resi 382-390
211chain B and backbone and resi 382-390

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUASNASNAA145 - 3926 - 253
21GLUGLUSERSERBB144 - 3905 - 251
12LEULEUASNASNAA145 - 3926 - 253
22GLUGLUSERSERBB144 - 3905 - 251
13LEULEUASNASNAA145 - 3926 - 253
23GLUGLUSERSERBB144 - 3905 - 251
14LEULEUASNASNAA145 - 3926 - 253
24GLUGLUSERSERBB144 - 3905 - 251
15LEULEUASNASNAA145 - 3926 - 253
25GLUGLUSERSERBB144 - 3905 - 251
16LEULEUASNASNAA145 - 3926 - 253
26GLUGLUSERSERBB144 - 3905 - 251
17LEULEUASNASNAA145 - 3926 - 253
27GLUGLUSERSERBB144 - 3905 - 251
18LEULEUASNASNAA145 - 3926 - 253
28GLUGLUSERSERBB144 - 3905 - 251
19LEULEUASNASNAA145 - 3926 - 253
29GLUGLUSERSERBB144 - 3905 - 251
110LEULEUASNASNAA145 - 3926 - 253
210GLUGLUSERSERBB144 - 3905 - 251
111LEULEUASNASNAA145 - 3926 - 253
211GLUGLUSERSERBB144 - 3905 - 251

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11

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Components

#1: Protein Probable two-component response regulator


Mass: 28152.180 Da / Num. of mol.: 2
Fragment: UNP residues 140-394, c-terminal phosphatase domain
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
Has protein modificationY

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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: 2.35 Å3/Da / Density % sol: 47.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.0 M Lithium Sulfate, 0.1 M MES, cryo-protected with 25% glycerol in well solution, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 5, 2007 / Details: crystal monochrometer
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1crystal monochromatorSINGLE WAVELENGTHMx-ray1
2crystal monochromatorMADMx-ray1
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
Reflection twinOperator: k,h,-l / Fraction: 0.506
ReflectionResolution: 2.95→13.95 Å / Num. all: 19831 / Num. obs: 19831 / % possible obs: 92.61 % / Redundancy: 4.3 % / Rsym value: 0.078

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementResolution: 2.95→13.95 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.654 / σ(F): 1.96 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.296 984 4.96 %
Rwork0.257 --
obs0.259 19831 92.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 76.999 Å2 / ksol: 0.233 e/Å3
Displacement parametersBiso max: 242.9 Å2 / Biso mean: 120.242 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-4.035 Å2-0 Å2-0 Å2
2--4.035 Å2-0 Å2
3----36.007 Å2
Refinement stepCycle: LAST / Resolution: 2.95→13.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3247 0 0 0 3247
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043297
X-RAY DIFFRACTIONf_angle_d0.7564467
X-RAY DIFFRACTIONf_chiral_restr0.055533
X-RAY DIFFRACTIONf_plane_restr0.005572
X-RAY DIFFRACTIONf_dihedral_angle_d12.4471143
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A144X-RAY DIFFRACTIONPOSITIONAL
12B144X-RAY DIFFRACTIONPOSITIONAL0.012
21A32X-RAY DIFFRACTIONPOSITIONAL
22B32X-RAY DIFFRACTIONPOSITIONAL0.049
31A128X-RAY DIFFRACTIONPOSITIONAL
32B128X-RAY DIFFRACTIONPOSITIONAL0.03
41A40X-RAY DIFFRACTIONPOSITIONAL
42B40X-RAY DIFFRACTIONPOSITIONAL0.024
51A36X-RAY DIFFRACTIONPOSITIONAL
52B36X-RAY DIFFRACTIONPOSITIONAL0.031
61A56X-RAY DIFFRACTIONPOSITIONAL
62B56X-RAY DIFFRACTIONPOSITIONAL0.052
71A24X-RAY DIFFRACTIONPOSITIONAL
72B24X-RAY DIFFRACTIONPOSITIONAL0.082
81A32X-RAY DIFFRACTIONPOSITIONAL
82B32X-RAY DIFFRACTIONPOSITIONAL0.117
91A20X-RAY DIFFRACTIONPOSITIONAL
92B20X-RAY DIFFRACTIONPOSITIONAL0.08
101A60X-RAY DIFFRACTIONPOSITIONAL
102B60X-RAY DIFFRACTIONPOSITIONAL0.051
111A36X-RAY DIFFRACTIONPOSITIONAL
112B36X-RAY DIFFRACTIONPOSITIONAL0.04
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10 / % reflection obs: 98 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.95-3.0550.39810.34411201201
3.055-3.1760.349850.35215691654
3.176-3.3180.3441180.34519042022
3.318-3.4910.343940.32920422136
3.491-3.7060.3651100.32520302140
3.706-3.9860.2871220.29819802102
3.986-4.3750.2891020.27420582160
4.375-4.9830.23820.22520242106
4.983-6.1860.267740.23721022176
6.186-13.950.29900.19620442134
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)
10.64761.4692-0.36370.5719-0.58010.4068-0.01680.8483-0.8627-1.1204-0.8102-0.4297-1.0046-0.325601.44290.03580.21351.2974-0.27021.2426-22.875950.23679.8676
23.0174-3.05891.83836.69446.86535.93250.4393-0.21010.4624-0.4860.069-0.2990.02620.5495-01.17470.08620.00310.98060.00250.9277-23.788428.21821.2427
35.2949-1.35990.57994.11573.09632.0564-0.02281.15750.2001-0.8686-0.05670.3232-0.1653-1.076-01.17230.02080.01291.27660.08010.9546-33.402729.8552-5.8062
40.21571.07070.64310.40930.28720.30660.9907-1.5565-2.21650.36210.50782.83830.428-3.10290.00041.28330.5103-0.24111.92110.13761.364-31.870846.428720.3276
57.886-2.76393.08024.8337-2.73165.86410.5221-0.2466-0.3076-0.00850.2040.55540.25080.2757-00.87840.01-0.07170.8592-0.01690.9606-12.059535.71229.1085
61.9999-0.30623.94673.2362-0.3032.264-1.01120.1230.27971.06340.6771-0.1007-1.96830.2847-01.79640.3148-0.05050.94480.05691.1232-10.538344.898838.3274
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resi 140-168
2X-RAY DIFFRACTION2chain A and resi 169-310
3X-RAY DIFFRACTION3chain A and resi 311-392
4X-RAY DIFFRACTION4chain B and resi 140-168
5X-RAY DIFFRACTION5chain B and resi 169-310
6X-RAY DIFFRACTION6chain B and resi 311-392

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