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- PDB-3heb: Crystal Structure of Response regulator receiver domain from Rhod... -

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Basic information

Entry
Database: PDB / ID: 3heb
TitleCrystal Structure of Response regulator receiver domain from Rhodospirillum rubrum
ComponentsResponse regulator receiver domain protein (CheY)Response regulator
Keywordstranscription regulator / NYSGXRC / PSI-II / receiver domain / respose regulator / 11237b / Protein structure Initiative / structural genomics / New York SGX Research Center for Structural Genomics
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
PHOSPHATE ION / Response regulator receiver domain protein (CheY)
Similarity search - Component
Biological speciesRhodospirillum rubrum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsSyed Ibrahim, B. / 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 domain from Rhodospirillum rubrum
Authors: Syed Ibrahim, B. / Burley, S.K. / Swaminathan, S.
History
DepositionMay 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _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: Response regulator receiver domain protein (CheY)
B: Response regulator receiver domain protein (CheY)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7904
Polymers34,6002
Non-polymers1902
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-22 kcal/mol
Surface area11960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.121, 75.071, 48.571
Angle α, β, γ (deg.)90.00, 96.41, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Response regulator receiver domain protein (CheY) / Response regulator


Mass: 17300.014 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodospirillum rubrum (bacteria) / Strain: ATCC 11170 / Gene: Rru_A0665 / Plasmid: TOP10 INVITROGEN / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q2RWM6
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.1 Å3/Da / Density % sol: 41.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M NaCl, 0.1 M Bis Tris pH 6.5, 25% Peg 3350, 3.0 M NDSB-195, 20 % Glycerol , VAPOR DIFFUSION, SITTING DROP, temperature 298 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9797 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 28, 2009 / Details: Mirrors
RadiationMonochromator: Si (III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionLowest resolution: 50 Å / Num. all: 11105 / Num. obs: 11105 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 11.5 Å2 / Rmerge(I) obs: 0.12 / Rsym value: 0.12 / Net I/σ(I): 7.6
Reflection shellResolution: 2.38→2.47 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 8.7 / Num. unique all: 969 / % possible all: 84.6

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Processing

Software
NameVersionClassification
CBASSdata collection
SHARPphasing
SHELXmodel building
ARP/wARPmodel building
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→35.21 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 59581.09 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.255 553 5.2 %RANDOM
Rwork0.203 ---
all0.203 11105 --
obs0.203 10607 94.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.6623 Å2 / ksol: 0.360488 e/Å3
Displacement parametersBiso mean: 20.3 Å2
Baniso -1Baniso -2Baniso -3
1--1.03 Å20 Å2-2.47 Å2
2---6.18 Å20 Å2
3---7.21 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 2.4→35.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2226 0 10 122 2358
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_mcbond_it1.251.5
X-RAY DIFFRACTIONc_mcangle_it1.962
X-RAY DIFFRACTIONc_scbond_it2.152
X-RAY DIFFRACTIONc_scangle_it3.152.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.273 67 4.1 %
Rwork0.194 1559 -
obs--87.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5po4.parampo4.top

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