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- PDB-3gl9: The structure of a histidine kinase-response regulator complex sh... -

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Basic information

Entry
Database: PDB / ID: 3gl9
TitleThe structure of a histidine kinase-response regulator complex sheds light into two-component signaling and reveals a novel cis autophosphorylation mechanism
ComponentsResponse regulator
KeywordsSIGNALING PROTEIN / beta-sheet / surrounded by alpha helices / both sides
Function / homology
Function and homology information


phosphorelay response regulator activity / phosphorelay signal transduction system / DNA binding / metal ion binding
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
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsCasino, P. / Rubio, V. / Marina, A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2009
Title: Structural Insight into Partner Specificity and Phosphoryl Transfer in Two-Component Signal Transduction
Authors: Casino, P. / Rubio, V. / Marina, A.
History
DepositionMar 11, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_asym_id / _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.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: 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
B: Response regulator
C: Response regulator
D: Response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,23113
Polymers55,6534
Non-polymers5789
Water11,764653
1
A: Response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0343
Polymers13,9131
Non-polymers1202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0343
Polymers13,9131
Non-polymers1202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0343
Polymers13,9131
Non-polymers1202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1304
Polymers13,9131
Non-polymers2163
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)155.233, 155.233, 34.482
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein
Response regulator / Response regulator RR468


Mass: 13913.255 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Plasmid: pET21d / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q9WYT9
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 653 / 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: 2.16 Å3/Da / Density % sol: 42.92 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 1.9M ammonium sulfate, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 18, 2008 / Details: Mirrors
RadiationMonochromator: horiz. foc. by sagittal curved 2nd crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→29.3 Å / Num. obs: 44647 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 10.7 % / Rmerge(I) obs: 0.073 / Rsym value: 0.33 / Net I/σ(I): 7.083
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.8-1.99.50.3332.26079864120.33399.2
1.9-2.019.80.2153.45992461160.21599.5
2.01-2.1510.20.1554.55900857660.15599.7
2.15-2.3210.80.1155.95737953360.11599.7
2.32-2.5511.20.0927.55531149380.092100
2.55-2.8511.70.0778.55269445210.077100
2.85-3.29120.0688.74745639710.068100
3.29-4.0211.60.05111.13932233990.051100
4.02-5.6911.30.03413.93021526760.034100
5.69-29.3411.60.0367.81759315120.03699.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.2.21data scaling
PHASERphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3DGE

3dge


Resolution: 1.8→25 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.919 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.874 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.148 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.237 2209 4.9 %RANDOM
Rwork0.185 ---
all0.188 ---
obs0.188 44636 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 57.14 Å2 / Biso mean: 16.99 Å2 / Biso min: 3.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20.15 Å20 Å2
2--0.3 Å20 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 1.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3901 0 29 653 4583
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223983
X-RAY DIFFRACTIONr_angle_refined_deg1.2142.0195371
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3615505
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.80425.641156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.00815836
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.211518
X-RAY DIFFRACTIONr_chiral_restr0.080.2636
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022798
X-RAY DIFFRACTIONr_nbd_refined0.2050.22196
X-RAY DIFFRACTIONr_nbtor_refined0.2990.22759
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2549
X-RAY DIFFRACTIONr_metal_ion_refined0.0360.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2280.2172
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1490.274
X-RAY DIFFRACTIONr_mcbond_it0.6821.52546
X-RAY DIFFRACTIONr_mcangle_it1.07923983
X-RAY DIFFRACTIONr_scbond_it1.75131606
X-RAY DIFFRACTIONr_scangle_it2.9014.51374
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0.005 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 2209 -
Rwork0.185 3063 -
all-3227 -
obs-44647 98.53 %

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