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- PDB-3kto: Crystal structure of response regulator receiver protein from Pse... -

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Basic information

Entry
Database: PDB / ID: 3kto
TitleCrystal structure of response regulator receiver protein from Pseudoalteromonas atlantica
ComponentsResponse regulator receiver protein
Keywordstranscription regulator / Response regulator receiver protein / PSI-II / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
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 speciesPseudoalteromonas atlantica T6c (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.98 Å
AuthorsDamodharan, L. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of response regulator receiver protein from Pseudoalteromonas atlantica
Authors: Damodharan, L. / Burley, S.K. / Swaminathan, S.
History
DepositionNov 25, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_conn
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Response regulator receiver protein
B: Response regulator receiver protein
C: Response regulator receiver protein


Theoretical massNumber of molelcules
Total (without water)46,3233
Polymers46,3233
Non-polymers00
Water5,026279
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Response regulator receiver protein


Theoretical massNumber of molelcules
Total (without water)15,4411
Polymers15,4411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Response regulator receiver protein


Theoretical massNumber of molelcules
Total (without water)15,4411
Polymers15,4411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: Response regulator receiver protein


Theoretical massNumber of molelcules
Total (without water)15,4411
Polymers15,4411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)116.333, 116.333, 169.701
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Detailsauthors state that the biological assembly is a trimer

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Components

#1: Protein Response regulator receiver protein


Mass: 15440.897 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudoalteromonas atlantica T6c (bacteria)
Strain: Strain T6c/BAA-1087 / Gene: Patl_2095 / Plasmid: pSGX3(BC) / Production host: Escherichia coli (E. coli) / References: UniProt: Q15U25
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / Source method: isolated from a natural source / Formula: H2O
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: 2.39 Å3/Da / Density % sol: 48.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M Sodium chloride, 0.1M HEPES pH 7.5, 25% w/v Polyethylene Glycol 3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 9, 2009 / Details: mirror
RadiationMonochromator: Si(111)channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. all: 30894 / Num. obs: 30894 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 24 % / Biso Wilson estimate: 34.6 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 12.5
Reflection shellResolution: 1.98→2.1 Å / Redundancy: 24.8 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 2 / Num. unique all: 4285 / % possible all: 88.5

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Processing

Software
NameVersionClassification
CBASSdata collection
SHARPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.98→40.55 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 102203.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1510 5.1 %RANDOM
Rwork0.218 ---
obs0.218 30705 96 %-
all-30894 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.9926 Å2 / ksol: 0.342456 e/Å3
Displacement parametersBiso mean: 32.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.62 Å22.39 Å20 Å2
2--1.62 Å20 Å2
3----3.24 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.98→40.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2815 0 0 279 3094
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_mcbond_it1.651.5
X-RAY DIFFRACTIONc_mcangle_it2.652
X-RAY DIFFRACTIONc_scbond_it2.522
X-RAY DIFFRACTIONc_scangle_it3.612.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 1.98→2.1 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.246 239 5.3 %
Rwork0.231 4285 -
obs-4285 88.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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