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- PDB-3lua: Crystal structure of a Signal receiver domain of Two component Si... -

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Basic information

Entry
Database: PDB / ID: 3lua
TitleCrystal structure of a Signal receiver domain of Two component Signal Transduction (Histidine Kinase) from Clostridium thermocellum
ComponentsResponse regulator receiver protein
KeywordsTranscription regulator / Two-component signal transduction system / Histidine Kinase / Phosphorelay / Receiver domain / 11201g / NYSGXRC / PSI-II / Structural Genomics / Protein Structure Initiative / 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 / Reverse transcriptase/Diguanylate cyclase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Stage 0 sporulation protein A homolog
Similarity search - Component
Biological speciesClostridium thermocellum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsSatyanarayana, L. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a Signal receiver domain of Two component Signal Transduction (Histidine Kinase) from Clostridium thermocellum
Authors: Satyanarayana, L. / Burley, S.K. / Swaminathan, S.
History
DepositionFeb 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 16, 2011Group: Atomic model
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Response regulator receiver protein


Theoretical massNumber of molelcules
Total (without water)16,4921
Polymers16,4921
Non-polymers00
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.100, 94.100, 68.009
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-177-

HOH

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Components

#1: Protein Response regulator receiver protein


Mass: 16491.611 Da / Num. of mol.: 1 / Fragment: signal receiver domain residues 2-130
Source method: isolated from a genetically manipulated source
Details: Top10 (Invitrogen) / Source: (gene. exp.) Clostridium thermocellum (bacteria) / Strain: ATCC 27405/DSM 1237 / Gene: 4809959, Cthe_3085 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Codon+RIL / References: UniProt: A3DK02
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.64 Å3/Da / Density % sol: 53.33 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M Sodium acetate pH 7.0, 20% PEG 3,350, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 26, 2009 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 26360 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.9 % / Biso Wilson estimate: 36.9 Å2 / Rsym value: 0.116 / Net I/σ(I): 6.2
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 10.5 % / Mean I/σ(I) obs: 5.6 / Num. unique all: 2615 / Rsym value: 0.779 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXCDphasing
SHARPphasing
CNS1.1refinement
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.4→47.05 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.267 545 -RANDOM
Rwork0.234 ---
all0.234 12710 --
obs0.234 12710 96.2 %-
Displacement parametersBiso mean: 40.9 Å2
Baniso -1Baniso -2Baniso -3
1--2.98 Å23.58 Å20 Å2
2---2.98 Å20 Å2
3---5.95 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.4→47.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1021 0 0 53 1074
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_degree24.6
X-RAY DIFFRACTIONc_improper_angle_deg0.85
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.04
RfactorNum. reflection% reflection
Rfree0.322 66 -
Rwork0.285 --
obs-1879 88.6 %

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