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- PDB-3f79: Structure of pseudo-centered cell crystal form of the C-terminal ... -

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Basic information

Entry
Database: PDB / ID: 3f79
TitleStructure of pseudo-centered cell crystal form of the C-terminal phosphatase domain of P. aeruginosa RssB
ComponentsProbable two-component response regulator
KeywordsSIGNALING PROTEIN / ADAPTOR
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 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_residues / software
Revision 1.3Sep 6, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
C: Probable two-component response regulator
D: Probable two-component response regulator
E: Probable two-component response regulator
F: Probable two-component response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,08313
Polymers168,9136
Non-polymers1707
Water00
1
A: Probable two-component response regulator
B: Probable two-component response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3293
Polymers56,3042
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Probable two-component response regulator
D: Probable two-component response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3775
Polymers56,3042
Non-polymers733
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Probable two-component response regulator
F: Probable two-component response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3775
Polymers56,3042
Non-polymers733
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)124.872, 124.872, 92.900
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-ID
11
21
31
41
51
61

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain F and backbone and (resi 151-235 or resi 249-258...
211chain A and backbone and (resi 151-235 or resi 249-258...
311chain B and backbone and (resi 151-235 or resi 249-258...
411chain C and backbone and (resi 151-235 or resi 249-258...
511chain D and backbone and (resi 151-235 or resi 249-258...
611chain E and backbone and (resi 151-235 or resi 249-258...

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.470928, -0.882002, -0.017302), (0.882076, -0.471076, 0.005516), (-0.013016, -0.012664, 0.999835)-1.84052, -72.760803, -61.692501
3given(-0.989169, -0.121312, -0.082626), (-0.117441, 0.991809, -0.050221), (0.088041, -0.039973, -0.995314)17.9722, -33.202599, -94.4729
4given(-0.513399, 0.85809, 0.010129), (-0.85812, -0.513247, -0.014446), (-0.007197, -0.016109, 0.999844)63.758301, -36.924198, -31.052299
5given(0.408778, 0.91006, -0.068496), (0.907799, -0.413181, -0.071992), (-0.093818, -0.032752, -0.995051)23.177099, -109.487999, -120.774002
6given(0.546442, -0.836319, -0.044406), (-0.837476, -0.546036, -0.021885), (-0.005945, 0.049148, -0.998774)-43.915798, -75.737396, -151.095993

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Components

#1: Protein
Probable two-component response regulator


Mass: 28152.180 Da / Num. of mol.: 6
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
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
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: 2.48 Å3/Da / Density % sol: 50.32 %

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Data collection

DiffractionMean temperature: 100 K
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 monochromonometer
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
Reflection twinType: merohedral / Operator: -k,-h,-l / Fraction: 0.498
ReflectionResolution: 2.8→50 Å / Num. obs: 78607 / % possible obs: 98.2 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 14.174
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
2.8-2.92.20.21187.2
2.9-3.022.50.19898.2
3.02-3.152.70.17799.6
3.15-3.322.80.14199.7
3.32-3.532.80.11599.6
3.53-3.82.80.09799.7
3.8-4.182.80.08799.9
4.18-4.792.80.07899.8
4.79-6.032.80.06399.8
6.03-502.80.04998.2

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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
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ES2

3es2


Resolution: 2.8→14.997 Å / Occupancy max: 1 / Occupancy min: 0 / σ(F): 2.01 / Phase error: 33.72 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2975 3912 5.02 %
Rwork0.2429 --
obs0.2455 77991 98.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.742 Å2 / ksol: 0.275 e/Å3
Displacement parametersBiso mean: 91.573 Å2
Baniso -1Baniso -2Baniso -3
1-8.666 Å2-0 Å2-0 Å2
2--8.666 Å2-0 Å2
3----34.435 Å2
Refinement stepCycle: LAST / Resolution: 2.8→14.997 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10379 0 7 0 10386
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310558
X-RAY DIFFRACTIONf_angle_d0.66914306
X-RAY DIFFRACTIONf_dihedral_angle_d13.9273718
X-RAY DIFFRACTIONf_chiral_restr0.0441680
X-RAY DIFFRACTIONf_plane_restr0.0031841
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11F708X-RAY DIFFRACTIONPOSITIONAL
12A708X-RAY DIFFRACTIONPOSITIONAL0.261
13B684X-RAY DIFFRACTIONPOSITIONAL0.29
14C724X-RAY DIFFRACTIONPOSITIONAL0.35
15D712X-RAY DIFFRACTIONPOSITIONAL0.324
16E720X-RAY DIFFRACTIONPOSITIONAL0.29
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.8480.3021870.3013118X-RAY DIFFRACTION98
2.848-2.89940.34231940.28553454X-RAY DIFFRACTION98
2.8994-2.95470.34941720.29433622X-RAY DIFFRACTION98
2.9547-3.01460.3322290.28183727X-RAY DIFFRACTION98
3.0146-3.07960.31832030.28743721X-RAY DIFFRACTION98
3.0796-3.15060.34672360.27193758X-RAY DIFFRACTION98
3.1506-3.22860.28321660.27243804X-RAY DIFFRACTION98
3.2286-3.3150.33391960.26743782X-RAY DIFFRACTION98
3.315-3.41140.28461850.27153759X-RAY DIFFRACTION98
3.4114-3.52020.3611730.25863744X-RAY DIFFRACTION98
3.5202-3.64430.28971720.25873761X-RAY DIFFRACTION98
3.6443-3.78790.24582070.2353803X-RAY DIFFRACTION98
3.7879-3.95730.30232110.24383662X-RAY DIFFRACTION98
3.9573-4.16170.27881880.23743830X-RAY DIFFRACTION98
4.1617-4.41620.29861680.2133802X-RAY DIFFRACTION98
4.4162-4.74710.27072030.19793743X-RAY DIFFRACTION98
4.7471-5.20660.24161940.20993797X-RAY DIFFRACTION98
5.2066-5.91910.28451960.24533745X-RAY DIFFRACTION98
5.9191-7.31070.44581860.28633767X-RAY DIFFRACTION98
7.3107-14.99680.26222050.20563721X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 21.24 Å / Origin y: -36.7611 Å / Origin z: -46.2241 Å
111213212223313233
T0.0442 Å2-0.0277 Å20.0121 Å2-0.0297 Å2-0.0064 Å2--0.0351 Å2
L0.037 °20.0343 °2-0.0136 °2--0.0045 °20.045 °2--0.0671 °2
S0.0341 Å °-0.0101 Å °-0.0005 Å °-0.0212 Å °-0.0074 Å °0.0024 Å °-0.0953 Å °0.0534 Å °0.0047 Å °
Refinement TLS groupSelection details: chain A or chain B or chain C or chain D or

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