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- PDB-1i3c: RESPONSE REGULATOR FOR CYANOBACTERIAL PHYTOCHROME, RCP1 -

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Basic information

Entry
Database: PDB / ID: 1i3c
TitleRESPONSE REGULATOR FOR CYANOBACTERIAL PHYTOCHROME, RCP1
ComponentsRESPONSE REGULATOR RCP1
KeywordsSIGNALING PROTEIN / Response regulator / Rcp1 / Phytochrome
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 Rcp1
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsIm, Y.J. / Rho, S.-H. / Park, C.-M. / Yang, S.-S. / Kang, J.-G. / Lee, J.Y. / Song, P.-S. / Eom, S.H.
CitationJournal: Protein Sci. / Year: 2002
Title: Crystal structure of a cyanobacterial phytochrome response regulator.
Authors: Im, Y.J. / Rho, S.H. / Park, C.M. / Yang, S.S. / Kang, J.G. / Lee, J.Y. / Song, P.S. / Eom, S.H.
History
DepositionFeb 14, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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

Downloads & links

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Assembly

Deposited unit
A: RESPONSE REGULATOR RCP1
B: RESPONSE REGULATOR RCP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3267
Polymers33,8462
Non-polymers4805
Water4,846269
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-76 kcal/mol
Surface area13010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.410, 76.990, 43.040
Angle α, β, γ (deg.)90.00, 106.15, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein RESPONSE REGULATOR RCP1


Mass: 16922.898 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Gene: SLR0474 / Plasmid: PTYB2 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: Q55169
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / 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: 1.95 Å3/Da / Density % sol: 36.8 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Ammonium Sulfate, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal grow
*PLUS
Temperature: 293-295 K
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1100 mMTris-HCl1reservoirpH8.5
23.1 Mammonium sulfate1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-18B10.9795
SYNCHROTRONPhoton Factory BL-18B20.9793
SYNCHROTRONPhoton Factory BL-18B30.95
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 15, 2000 / Details: Quartz crystal
RadiationMonochromator: Quartz crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97931
30.951
ReflectionResolution: 1.9→14.97 Å / Num. all: 20164 / Num. obs: 83143 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 4 / Redundancy: 4 % / Biso Wilson estimate: 10.1 Å2 / Limit h max: 20 / Limit h min: -21 / Limit k max: 40 / Limit k min: -21 / Limit l max: 22 / Limit l min: 0 / Observed criterion F max: 892718.68 / Observed criterion F min: 7.4 / Rmerge(I) obs: 0.046 / Net I/σ(I): 12.8
Reflection shellResolution: 1.9→1.99 Å / Redundancy: 4 % / Rmerge(I) obs: 0.155 / % possible all: 98.5
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 15 Å / Num. obs: 20025 / Num. measured all: 83143
Reflection shell
*PLUS
% possible obs: 98.5 %

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Processing

Software
NameVersionClassification
SHARPphasing
CNS1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.9→14.97 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 4 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1987 9.9 %RANDOM
Rwork0.188 ---
all0.19 20453 --
obs0.19 20149 98.5 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 42.347 Å2 / ksol: 0.391785 e/Å3
Displacement parametersBiso max: 56.2 Å2 / Biso mean: 14.51 Å2 / Biso min: 1.48 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20.41 Å2
2--0.52 Å20 Å2
3----0.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.08 Å
Luzzati d res high-1.9
Refinement stepCycle: LAST / Resolution: 1.9→14.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2256 0 25 269 2550
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_torsion_deg22.4
X-RAY DIFFRACTIONx_torsion_impr_deg0.9
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
1.9-1.990.2192399.40.22122270.0142543246697
1.99-2.090.1832389.40.18422470.0122542248597.8
2.09-2.220.18326610.40.18322320.0112554249897.8
2.22-2.390.1825910.10.17922650.0112560252498.6
2.39-2.630.1882359.20.18822720.0122541250798.6
2.63-3.010.2042449.50.20422920.0132571253698.6
3.01-3.780.1862379.30.18523050.0122557254299.4
3.78-14.970.17726910.30.17823220.0112605259199.4
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 15 Å / σ(F): 2 / % reflection Rfree: 9.9 % / Rfactor obs: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 14.5 Å2
LS refinement shell
*PLUS
Rfactor Rfree: 0.219 / % reflection Rfree: 9.4 % / Rfactor Rwork: 0.221

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