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- PDB-3a10: Crystal structure of response regulator protein TrrA (TM1360) fro... -

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Basic information

Entry
Database: PDB / ID: 3a10
TitleCrystal structure of response regulator protein TrrA (TM1360) from Thermotoga maritima in complex with Mg(2+)-BeF (SeMet, L89M)
ComponentsResponse regulator
KeywordsSIGNALING PROTEIN / phosphoacceptor
Function / homology
Function and homology information


phosphorelay signal transduction system / DNA binding / metal ion binding
Similarity search - Function
Transcriptional regulatory protein WalR-like / 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
BERYLLIUM TRIFLUORIDE ION / Response regulator
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.63 Å
AuthorsYamada, S. / Sugimoto, H. / Kobayashi, M. / Ohno, A. / Nakamura, H. / Shiro, Y.
CitationJournal: Structure / Year: 2009
Title: Structure of PAS-linked histidine kinase and the response regulator complex
Authors: Yamada, S. / Sugimoto, H. / Kobayashi, M. / Ohno, A. / Nakamura, H. / Shiro, Y.
History
DepositionMar 25, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0005
Polymers13,5211
Non-polymers4794
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.678, 32.678, 199.242
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Response regulator


Mass: 13520.953 Da / Num. of mol.: 1 / Mutation: L89MSE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM_1360 / Plasmid: pRSETA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) CodonPlus RIL / References: UniProt: Q9X181
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 1.97 Å3/Da / Density % sol: 37.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.2
Details: 50% PEG200, 0.1M sodium/potassium-phosphate, 0.1M sodium chloride, pH 6.2, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 0.9795,0.9797,0.9787
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Mar 14, 2006
RadiationMonochromator: DIAMOND 111 DOUBLE CRYSTAL MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97971
30.97871
ReflectionResolution: 1.63→50 Å / Num. obs: 14298 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 18.8 Å2 / Rsym value: 0.037 / Net I/σ(I): 43.7
Reflection shellResolution: 1.63→1.69 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 8.9 / Rsym value: 0.143 / % possible all: 99.8

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.63→20 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.929 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 2.014 / SU ML: 0.071 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.116 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25 719 5 %RANDOM
Rwork0.2 ---
obs0.203 14289 98.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 49.85 Å2 / Biso mean: 19.765 Å2 / Biso min: 8.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20 Å2
2---0.17 Å20 Å2
3---0.35 Å2
Refinement stepCycle: LAST / Resolution: 1.63→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms968 0 31 106 1105
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221010
X-RAY DIFFRACTIONr_angle_refined_deg1.4462.0181344
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9985121
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.86925.8746
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.65515207
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.483154
X-RAY DIFFRACTIONr_chiral_restr0.0810.2146
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02716
X-RAY DIFFRACTIONr_nbd_refined0.210.2461
X-RAY DIFFRACTIONr_nbtor_refined0.3060.2692
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.289
X-RAY DIFFRACTIONr_metal_ion_refined0.0970.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.250.272
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.217
X-RAY DIFFRACTIONr_mcbond_it1.0021.5618
X-RAY DIFFRACTIONr_mcangle_it1.392957
X-RAY DIFFRACTIONr_scbond_it2.4233443
X-RAY DIFFRACTIONr_scangle_it3.7194.5385
LS refinement shellResolution: 1.631→1.673 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 60 -
Rwork0.245 929 -
all-989 -
obs--99 %

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