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- PDB-5te9: Crystal structure of a response regulator receiver protein from B... -

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Basic information

Entry
Database: PDB / ID: 5te9
TitleCrystal structure of a response regulator receiver protein from Burkholderia phymatum
ComponentsResponse regulator receiver protein
KeywordsSIGNALING PROTEIN / structural genomics / SSGCID / NIAID / proteobacteria / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


phosphorelay signal transduction system
Similarity search - Function
: / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Response regulator receiver protein
Similarity search - Component
Biological speciesParaburkholderia phymatum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.401 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal structure of a response regulator receiver protein from Burkholderia phymatum
Authors: Edwards, T.E. / Delker, S.L. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionSep 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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 / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Response regulator receiver protein


Theoretical massNumber of molelcules
Total (without water)17,9261
Polymers17,9261
Non-polymers00
Water19811
1
A: Response regulator receiver protein

A: Response regulator receiver protein


Theoretical massNumber of molelcules
Total (without water)35,8512
Polymers35,8512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area2630 Å2
ΔGint-16 kcal/mol
Surface area13060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.390, 103.840, 55.470
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Response regulator receiver protein


Mass: 17925.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paraburkholderia phymatum (strain DSM 17167 / CIP 108236 / LMG 21445 / STM815) (bacteria)
Strain: DSM 17167 / CIP 108236 / LMG 21445 / STM815 / Gene: Bphy_1144 / Production host: Escherichia coli (E. coli) / References: UniProt: B2JH95
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O

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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: 2.31 Å3/Da / Density % sol: 46.64 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: BuphA.00051.b.B1.PS37982 at 35 mg/mL against MCSG1 screen condition E4, 0.2 M Li2SO4, 0.1 M Tris pH 8.5, 25% PEG 3350 supplemented with 20% EG as cryo-protectant

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 6748 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 47.44 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Net I/σ(I): 19.51
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
2.4-2.460.5673.750.9071100
2.46-2.530.5094.060.923199.8
2.53-2.60.375.480.9681100
2.6-2.680.3545.580.963199.6
2.68-2.770.2647.230.985199.5
2.77-2.870.2368.460.9841100
2.87-2.980.15911.790.9911100
2.98-3.10.12114.60.996199.8
3.1-3.240.09717.550.996199.5
3.24-3.40.07522.110.9981100
3.4-3.580.05527.20.998199.7
3.58-3.80.0529.980.9981100
3.8-4.060.04434.680.999199.7
4.06-4.380.03640.360.999199.3
4.38-4.80.03441.350.9991100
4.8-5.370.03741.920.9991100
5.37-6.20.03839.340.9981100
6.2-7.590.03840.150.998199.5
7.59-10.740.03745.520.9991100
10.74-500.03741.910.998195.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
MOLREPphasing
PHENIXdev_2499refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BRI, chain A

5bri
PDB Unreleased entry


Resolution: 2.401→37.906 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.45
RfactorNum. reflection% reflection
Rfree0.2693 707 10.48 %
Rwork0.2012 --
obs0.2086 6743 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 117.44 Å2 / Biso mean: 62.383 Å2 / Biso min: 28.76 Å2
Refinement stepCycle: final / Resolution: 2.401→37.906 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1065 0 0 11 1076
Biso mean---55.78 -
Num. residues----137
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071087
X-RAY DIFFRACTIONf_angle_d0.851482
X-RAY DIFFRACTIONf_chiral_restr0.054177
X-RAY DIFFRACTIONf_plane_restr0.006190
X-RAY DIFFRACTIONf_dihedral_angle_d15.627656
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.4007-2.5860.34951160.270312031319
2.586-2.84620.32421450.24711751320
2.8462-3.25780.29451530.230811851338
3.2578-4.10370.26061510.198211981349
4.1037-37.91060.24191420.173712751417
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)
18.89830.8458-2.43435.52081.64786.4210.50871.2186-0.55350.0306-0.5395-0.00250.0763-1.02650.05410.38240.07170.01570.6549-0.00880.2579-20.9052-19.71941.1642
26.63760.97-0.01423.80431.78855.8010.29361.52830.6693-0.2370.0601-0.6184-0.24750.6665-0.27470.40470.07740.07350.67960.13620.4836-12.7037-12.92220.0413
39.58-2.86510.83818.7797-0.14415.28940.1180.04380.29430.6458-0.0472-0.92020.23670.92840.01040.44410.0935-0.05980.6322-0.08350.3659-7.0276-20.89759.9976
49.2608-1.5899-2.17648.44010.57946.1206-0.1031-0.25050.50370.36860.3463-0.43720.44060.3206-0.18910.438-0.11520.02380.64040.05880.2457-23.9635-16.515614.9883
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 31 )A8 - 31
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 76 )A32 - 76
3X-RAY DIFFRACTION3chain 'A' and (resid 77 through 124 )A77 - 124
4X-RAY DIFFRACTION4chain 'A' and (resid 125 through 146 )A125 - 146

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