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- PDB-5cos: Crystal Structure of the Cytoplasmic Domain of the Pseudomonas pu... -

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Basic information

Entry
Database: PDB / ID: 5cos
TitleCrystal Structure of the Cytoplasmic Domain of the Pseudomonas putida Anti-sigma Factor PupR
ComponentsSiderophore-interacting protein
KeywordsTRANSCRIPTION
Function / homologyFecR, N-terminal / Domain of unknown function (DUF4880) / FecR protein / Fe(2+)-dicitrate sensor, transmembrane component / FecR protein / Siderophore-interacting protein
Function and homology information
Biological speciesPseudomonas sp. WCS358 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.019 Å
AuthorsJensen, J.L. / Colbert, C.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R15GM113227-01 United States
CitationJournal: Biochemistry / Year: 2015
Title: Mechanistic Implications of the Unique Structural Features and Dimerization of the Cytoplasmic Domain of the Pseudomonas Sigma Regulator, PupR.
Authors: Jensen, J.L. / Balbo, A. / Neau, D.B. / Chakravarthy, S. / Zhao, H. / Sinha, S.C. / Colbert, C.L.
History
DepositionJul 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references
Revision 1.2Sep 20, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Siderophore-interacting protein
B: Siderophore-interacting protein
C: Siderophore-interacting protein
D: Siderophore-interacting protein


Theoretical massNumber of molelcules
Total (without water)38,0594
Polymers38,0594
Non-polymers00
Water1,856103
1
C: Siderophore-interacting protein
D: Siderophore-interacting protein


Theoretical massNumber of molelcules
Total (without water)19,0302
Polymers19,0302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Siderophore-interacting protein
B: Siderophore-interacting protein


Theoretical massNumber of molelcules
Total (without water)19,0302
Polymers19,0302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-21 kcal/mol
Surface area7090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.459, 134.621, 34.896
Angle α, β, γ (deg.)90.00, 113.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Siderophore-interacting protein / PupR protein


Mass: 9514.770 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. WCS358 (bacteria) / Gene: PC358_08100 / Plasmid: pMBP-Parallel1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: A0A084CH09
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.86 Å3/Da / Density % sol: 33.9 % / Description: thin, rod-like clusters
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 100mM Bis-Tris pH 6.0, 3M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.019→44.87 Å / Num. obs: 18320 / % possible obs: 98.8 % / Redundancy: 3.4 % / Net I/σ(I): 13.3
Reflection shellResolution: 2.02→2.13 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.4 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CAM

5cam


Resolution: 2.019→33.655 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2573 1017 5.56 %
Rwork0.2155 --
obs0.2177 18281 98.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.019→33.655 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1869 0 0 103 1972
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011985
X-RAY DIFFRACTIONf_angle_d1.1832709
X-RAY DIFFRACTIONf_dihedral_angle_d15.607728
X-RAY DIFFRACTIONf_chiral_restr0.054280
X-RAY DIFFRACTIONf_plane_restr0.006355
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0192-2.12560.30511350.26692484X-RAY DIFFRACTION99
2.1256-2.25880.28421650.23782453X-RAY DIFFRACTION99
2.2588-2.43310.24891510.23352467X-RAY DIFFRACTION99
2.4331-2.67790.27321550.23172494X-RAY DIFFRACTION99
2.6779-3.06520.28321350.23082460X-RAY DIFFRACTION99
3.0652-3.86090.23541450.20412444X-RAY DIFFRACTION98
3.8609-33.65990.24811310.19892462X-RAY DIFFRACTION97
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)
13.40080.79580.85270.81271.50293.0642-0.08010.22370.20281.00130.4766-1.1504-0.45810.42610.13831.0364-0.0892-0.02280.33610.02870.591129.108924.06654.0191
21.6968-0.11780.52850.78920.57860.6660.46120.0040.56360.92770.4351-0.8297-1.51160.34730.06681.0397-0.0380.15980.415-0.00930.566626.215814.6922.8412
30.5797-0.1481-0.39861.06630.22960.9714-0.6798-0.0993-0.03080.22070.25380.93680.876-0.6057-0.01391.0159-0.12890.04780.45740.0040.754219.344527.74480.4829
41.8832-0.7988-0.35950.7657-0.17450.283-0.25870.1450.25760.81420.07780.48280.5623-0.11710.04660.9518-0.0903-0.04820.2942-0.0180.49222.593743.30073.4234
54.18450.65860.15540.15710.01420.1114-0.88020.43440.02060.59710.1281-0.88580.21020.1234-0.49720.9689-0.0376-0.01350.30560.0690.671630.78234.59950.5764
60.2139-0.46280.02341.31410.71373.817-0.14320.5528-0.44270.2212-0.19890.52660.0385-1.4963-0.20670.19790.0466-0.02020.50010.00950.286233.589766.47332.3117
70.56480.01380.00791.1994-0.24170.51860.25090.30730.5734-0.09350.035-0.0603-0.49940.10920.0830.23460.02590.0250.440.06280.312142.49369.1323-0.4133
81.29050.38960.20240.6931-0.16162.07470.31410.2875-0.71250.28340.0377-0.26421.1404-0.09140.01880.4035-0.0346-0.07090.41270.03860.393136.079456.31314.3036
92.22670.2801-1.08522.17240.64041.70450.0579-0.3438-0.25380.1555-0.10220.19330.2535-0.3157-0.00640.1934-0.0004-0.00740.36460.03120.280820.781562.2021-1.6085
101.8732-0.56190.0250.5952-0.11182.06640.2947-0.55840.6346-0.3610.2203-0.2292-1.0234-0.17270.0470.37090.04090.07310.3672-0.03090.350319.12873.1182-3.7905
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 25 )
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 44 )
3X-RAY DIFFRACTION3chain 'A' and (resid 45 through 65 )
4X-RAY DIFFRACTION4chain 'B' and (resid 11 through 44 )
5X-RAY DIFFRACTION5chain 'B' and (resid 45 through 65 )
6X-RAY DIFFRACTION6chain 'C' and (resid 8 through 25 )
7X-RAY DIFFRACTION7chain 'C' and (resid 26 through 44 )
8X-RAY DIFFRACTION8chain 'C' and (resid 45 through 65 )
9X-RAY DIFFRACTION9chain 'D' and (resid 5 through 44 )
10X-RAY DIFFRACTION10chain 'D' and (resid 45 through 65 )

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