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- PDB-4jau: Structural basis of a rationally rewired protein-protein interfac... -

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Basic information

Entry
Database: PDB / ID: 4jau
TitleStructural basis of a rationally rewired protein-protein interface (HK853mutant A268V, A271G, T275M, V294T and D297E)
ComponentsHistidine kinase
KeywordsTRANSFERASE / Bergerat fold / Four-helix bundle / Signal transduction / Histidine kinase / Autophosphorylation / Phosphatase / Response regulator RR468
Function / homology
Function and homology information


histidine phosphotransfer kinase activity / histidine kinase / phosphorelay sensor kinase activity / nucleotide binding / identical protein binding / metal ion binding
Similarity search - Function
Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 ...Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Helix Hairpins / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / histidine kinase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsPodgornaia, A.I. / Casino, P. / Marina, A. / Laub, M.T.
CitationJournal: Structure / Year: 2013
Title: Structural basis of a rationally rewired protein-protein interface critical to bacterial signaling
Authors: Podgornaia, A.I. / Casino, P. / Marina, A. / Laub, M.T.
History
DepositionFeb 19, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2013Group: Database references / Structure summary
Revision 1.2Nov 8, 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 / 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_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

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Assembly

Deposited unit
A: Histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8662
Polymers29,4381
Non-polymers4271
Water77543
1
A: Histidine kinase
hetero molecules

A: Histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7314
Polymers58,8772
Non-polymers8542
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5370 Å2
ΔGint-39 kcal/mol
Surface area23860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.962, 160.377, 43.885
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-631-

HOH

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Components

#1: Protein Histidine kinase / Sensor histidine kinase


Mass: 29438.402 Da / Num. of mol.: 1 / Fragment: HK853 cytoplasmic region, UNP residues 232-489 / Mutation: A268V, A271G, T275M, V294T, D297E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: TM_0853 / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): K-12 / References: UniProt: Q9WZV7, histidine kinase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.45 Å3/Da / Density % sol: 49.78 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 8% PEG4000, 0.8M lithium chloride, Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 10, 2011 / Details: toroidal mirrors
RadiationMonochromator: Single bounce monochromator 28m / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 2.7→73 Å / Num. obs: 8277 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.057
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.337 / Mean I/σ(I) obs: 21 / Num. unique all: 8277 / Rsym value: 0.337 / % possible all: 99.5

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2C2A

2c2a


Resolution: 2.7→44.78 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.903 / SU B: 35.712 / SU ML: 0.373 / Cross valid method: THROUGHOUT / σ(F): 2.3 / ESU R Free: 0.392 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27977 579 7 %RANDOM
Rwork0.23599 ---
obs0.23913 8277 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 70.365 Å2
Baniso -1Baniso -2Baniso -3
1-1.15 Å20 Å20 Å2
2---1.92 Å20 Å2
3---0.77 Å2
Refinement stepCycle: LAST / Resolution: 2.7→44.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1864 0 27 43 1934
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191954
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.31.9892650
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6655238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.09124.73795
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.20515365
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3461513
X-RAY DIFFRACTIONr_chiral_restr0.0840.2302
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211445
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellHighest resolution: 2.7 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 579 -
Rwork0.236 470 -
obs-60367 99.5 %
Refinement TLS params.Method: refined / Origin x: -18.8408 Å / Origin y: 17.9942 Å / Origin z: -4.4024 Å
111213212223313233
T0.3589 Å20.1188 Å20.086 Å2-0.1293 Å2-0.0056 Å2--0.3624 Å2
L1.9162 °20.7865 °20.0921 °2-0.4739 °20.3746 °2--1.8787 °2
S0.1378 Å °-0.1549 Å °0.2816 Å °-0.0298 Å °-0.0572 Å °-0.0681 Å °-0.3749 Å °-0.2001 Å °-0.0806 Å °

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