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- PDB-1k66: Crystal Structure of the Cyanobacterial Phytochrome Response Regu... -

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Basic information

Entry
Database: PDB / ID: 1k66
TitleCrystal Structure of the Cyanobacterial Phytochrome Response Regulator, RcpB
ComponentsPhytochrome Response Regulator RcpB
KeywordsSIGNALING PROTEIN / Response Regulator / CheY homologue / homodimer / apo-protein / (beta/alpha)5
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
BETA-MERCAPTOETHANOL / Response regulator
Similarity search - Component
Biological speciesTolypothrix sp. PCC 7601 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.75 Å
AuthorsBenda, C. / Scheufler, C. / Tandeau de Marsac, N. / Gaertner, W.
CitationJournal: Biophys.J. / Year: 2004
Title: Crystal structures of two cyanobacterial response regulators in apo- and phosphorylated form reveal a novel dimerization motif of phytochrome-associated response regulators
Authors: Benda, C. / Scheufler, C. / Tandeau de Marsac, N. / Gaertner, W.
History
DepositionOct 15, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phytochrome Response Regulator RcpB
B: Phytochrome Response Regulator RcpB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6703
Polymers33,5922
Non-polymers781
Water7,080393
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-14 kcal/mol
Surface area13380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.180, 72.180, 142.782
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Cell settingtetragonal
Space group name H-MP41212

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Components

#1: Protein Phytochrome Response Regulator RcpB


Mass: 16796.145 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tolypothrix sp. PCC 7601 (bacteria) / Gene: AF309560 / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Gold, Novagen / References: UniProt: Q8RTM8
#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 393 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 48.7 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, magnesium chloride, tris buffer, glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP at 280K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
13.75 Msodium formate1reservoir
25 %(v/v)glycerol1reservoir
31 mM2-mercaptoethanol1reservoir
43-5 mg/mlprotein1drop
5150 mM1dropNaCl
610 mMTris-HCl1droppH8.0
75 %(v/v)glycerol1drop
81 mM2-mercaptoethanol1drop

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONMPG/DESY, HAMBURG BW610.9800, 0.9811, 0.9500, 1.05
ROTATING ANODERIGAKU21.5418
Detector
TypeIDDetectorDate
MARRESEARCH1CCDMar 20, 2001
MARRESEARCH2IMAGE PLATE
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.981
20.98111
30.951
41.051
51.54181
ReflectionResolution: 1.75→14.52 Å / Num. all: 37955 / Num. obs: 37955 / Observed criterion σ(I): 0 / Biso Wilson estimate: 22.2 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 27.4
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 39024 / % possible obs: 98.2 % / Num. measured all: 260719
Reflection shell
*PLUS
Highest resolution: 1.75 Å / Lowest resolution: 3.9 Å / % possible obs: 98.8 % / Rmerge(I) obs: 0.122 / Mean I/σ(I) obs: 12.2

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
CNSrefinement
RefinementResolution: 1.75→14.52 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1616477.01 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.25 3771 9.9 %RANDOM
Rwork0.216 ---
obs0.2161 37955 97.6 %-
all-37955 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 81.0128 Å2 / ksol: 0.473444 e/Å3
Displacement parametersBiso mean: 26 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20 Å20 Å2
2--0.52 Å20 Å2
3----1.05 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.75→14.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2353 0 4 393 2750
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.75→1.86 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.272 642 10.1 %
Rwork0.248 5704 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4BME_XPLOR.PARBME_XPLOR.TOP
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rfree: 0.243 / Rfactor Rwork: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83

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