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

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Basic information

Entry
Database: PDB / ID: 5cam
TitleCrystal Structure of the Cytoplasmic Domain of the Pseudomonas putida Anti-sigma Factor PupR (SeMet)
ComponentsPupR proteinPolytechnic University of Puerto Rico
KeywordsTRANSCRIPTION / Bacterial Proteins / Membrane Proteins / Cytoplasm / Sigma Factor / Transcription Factors / Gene Expression Regulation
Function / homologyFecR, N-terminal / Domain of unknown function (DUF4880) / FecR protein / Fe(2+)-dicitrate sensor, transmembrane component / FecR protein / sigma factor antagonist activity / PupR protein
Function and homology information
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.171 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
DepositionJun 29, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PupR protein
B: PupR protein
C: PupR protein
D: PupR protein


Theoretical massNumber of molelcules
Total (without water)38,9974
Polymers38,9974
Non-polymers00
Water1,72996
1
C: PupR protein
D: PupR protein


Theoretical massNumber of molelcules
Total (without water)19,4982
Polymers19,4982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: PupR protein
B: PupR protein


Theoretical massNumber of molelcules
Total (without water)19,4982
Polymers19,4982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-21 kcal/mol
Surface area6700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.491, 134.691, 34.903
Angle α, β, γ (deg.)90.00, 113.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
PupR protein / Polytechnic University of Puerto Rico


Mass: 9749.245 Da / Num. of mol.: 4 / Fragment: Residues 1-82
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: loc5358 / Gene: pupR / Plasmid: pMBP-Parallel-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q52209
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 1.85 Å3/Da / Density % sol: 33.42 %
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-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.17→134.7 Å / Num. obs: 14546 / % possible obs: 97.2 % / Redundancy: 6.9 % / Net I/σ(I): 18.2
Reflection shellResolution: 2.17→2.29 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 1.7 / % possible all: 82

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata reduction
SCALAdata scaling
PHENIXAutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.171→67.346 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.16 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2165 1434 10.12 %
Rwork0.1779 --
obs0.1818 14172 94.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.6 Å2
Refinement stepCycle: LAST / Resolution: 2.171→67.346 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1849 0 0 96 1945
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0181971
X-RAY DIFFRACTIONf_angle_d1.5112687
X-RAY DIFFRACTIONf_dihedral_angle_d17.928719
X-RAY DIFFRACTIONf_chiral_restr0.077275
X-RAY DIFFRACTIONf_plane_restr0.009352
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1706-2.24820.43931020.3411880X-RAY DIFFRACTION66
2.2482-2.33820.30621410.28091221X-RAY DIFFRACTION91
2.3382-2.44460.27151440.21481278X-RAY DIFFRACTION97
2.4446-2.57350.20981490.18941322X-RAY DIFFRACTION98
2.5735-2.73470.18541420.17741326X-RAY DIFFRACTION99
2.7347-2.94590.23621540.18261338X-RAY DIFFRACTION100
2.9459-3.24230.2131500.18471332X-RAY DIFFRACTION100
3.2423-3.71150.23091470.1631356X-RAY DIFFRACTION100
3.7115-4.67590.17831520.13811345X-RAY DIFFRACTION100
4.6759-67.37790.19181530.171340X-RAY DIFFRACTION99
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)
19.44722.96413.26838.59475.77574.0786-0.18170.00621.14641.03780.059-1.2627-1.19870.7933-0.28181.2444-0.1247-0.1440.38450.01730.833429.170423.75994.1397
26.97014.89851.90684.3167-0.71176.4207-0.27041.23290.412-0.99590.5472-1.4213-1.96120.626-0.09950.9559-0.20120.23080.5631-0.06090.623930.248416.7914-7.3064
36.5678-1.0668-1.15482.18681.37810.9057-0.10920.05950.77341.4550.35430.4551-0.8726-0.2766-0.06241.01840.00550.05510.26870.0680.647724.030314.02376.3149
48.7376-2.61453.16824.43012.98815.9596-0.98680.310.38431.3104-0.32081.1131-0.6692-0.00511.14931.0423-0.08950.0390.3701-0.02160.882219.717727.80560.6108
55.8565-3.25921.64883.701-3.54995.0197-0.08630.0923-0.14190.03830.43941.60440.947-0.9285-0.15651.0676-0.0218-0.0550.422-0.05640.802920.826140.12421.333
67.3895-0.5693-2.47075.5628-2.25352.5335-0.563-0.38740.07561.57670.177-1.11160.42960.1830.44690.9459-0.0645-0.13290.33820.0520.623928.810140.17553.6241
75.0515-0.722-1.17324.7450.09182.91960.0890.58180.06160.06420.00750.8405-0.1677-1.63920.00090.20550.0112-0.00830.50010.00440.33534.773165.7640.6394
84.69511.593-0.28154.4040.41255.97190.1330.1687-0.53080.048-0.0056-0.61870.62340.2858-0.13340.20270.0747-0.0610.25450.00250.277638.740561.08343.8069
95.32760.6821-1.26876.07931.0268.2547-0.0037-0.5617-0.16870.1871-0.00160.25650.3-0.35590.05030.17820.0096-0.00880.36260.0450.332421.273362.0803-1.1552
108.412-3.8469-2.55746.50072.77757.48850.0765-0.68591.0655-0.00430.25530.1652-1.26830.2759-0.38280.3696-0.03560.04260.2724-0.04510.394219.232173.4026-4.0536
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 24 )
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 30 )
3X-RAY DIFFRACTION3chain 'A' and (resid 31 through 44 )
4X-RAY DIFFRACTION4chain 'A' and (resid 45 through 65 )
5X-RAY DIFFRACTION5chain 'B' and (resid 11 through 30 )
6X-RAY DIFFRACTION6chain 'B' and (resid 31 through 64 )
7X-RAY DIFFRACTION7chain 'C' and (resid 7 through 30 )
8X-RAY DIFFRACTION8chain 'C' and (resid 31 through 65 )
9X-RAY DIFFRACTION9chain 'D' and (resid 7 through 44 )
10X-RAY DIFFRACTION10chain 'D' and (resid 45 through 65 )

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