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- PDB-6qrj: Crystal structure of ShkA full-length in complex with AMPPNP -

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Basic information

Entry
Database: PDB / ID: 6qrj
TitleCrystal structure of ShkA full-length in complex with AMPPNP
ComponentsHybrid kinase
KeywordsSIGNALING PROTEIN / Cyclic di-GMP / second messenger / hybride histidine kinase / ShkA / auto-inhibitio
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity
Similarity search - Function
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. / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver 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. / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / histidine kinase
Similarity search - Component
Biological speciesCaulobacter vibrioides CB15 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsDubey, B.N. / Schirmer, T.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_166652 Switzerland
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Hybrid histidine kinase activation by cyclic di-GMP-mediated domain liberation.
Authors: Dubey, B.N. / Agustoni, E. / Bohm, R. / Kaczmarczyk, A. / Mangia, F. / von Arx, C. / Jenal, U. / Hiller, S. / Plaza-Menacho, I. / Schirmer, T.
History
DepositionFeb 19, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hybrid kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8313
Polymers50,3001
Non-polymers5312
Water19811
1
A: Hybrid kinase
hetero molecules

A: Hybrid kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,6626
Polymers100,6012
Non-polymers1,0614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x,y,-z1
Buried area4880 Å2
ΔGint-54 kcal/mol
Surface area40530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.504, 64.504, 260.209
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein Hybrid kinase / Sensor histidine kinase/response regulator


Mass: 50300.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter vibrioides CB15 (bacteria) / Gene: shkA, CC_0138, CC0138 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ABT2
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.69 Å3/Da / Density % sol: 54.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M DL-Serine, 0.1M Sodium HEPES pH 7.5, MOPS (acid), 40% v/v ethylene glycol and 20% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00004 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 2.64→20 Å / Num. obs: 17058 / % possible obs: 99 % / Observed criterion σ(F): 1.05 / Redundancy: 12.7 % / CC1/2: 1 / Rmerge(I) obs: 0.01 / Rpim(I) all: 0.03 / Net I/σ(I): 17
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) all% possible allRrim(I) all
2.64-2.87.0270.010.8650220.4820.0399.2
2.99-3.237.450.4943.9144170.9451000.531
3.23-3.537.3560.2667.3940110.9831000.287
3.53-3.957.1490.16512.4336220.99299.60.178
3.95-4.556.6080.0781732240.99799.90.085
4.55-5.567.2390.0611727180.9981000.066
5.56-7.816.8590.05332.2721170.99999.90.057
7.81-206.2840.0349.251220199.30.033

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4q20

4q20


Resolution: 2.65→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.941 / SU B: 41.842 / SU ML: 0.363 / SU R Cruickshank DPI: 0.7124 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.712 / ESU R Free: 0.343
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2747 843 5 %RANDOM
Rwork0.2166 ---
obs0.2196 16013 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 173.72 Å2 / Biso mean: 82.808 Å2 / Biso min: 46.09 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20 Å20 Å2
2--0.35 Å20 Å2
3----0.7 Å2
Refinement stepCycle: final / Resolution: 2.65→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3383 0 32 11 3426
Biso mean--67.92 69.16 -
Num. residues----463
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0133462
X-RAY DIFFRACTIONr_bond_other_d0.0040.0173405
X-RAY DIFFRACTIONr_angle_refined_deg1.9251.6384710
X-RAY DIFFRACTIONr_angle_other_deg1.3021.5727808
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.6215459
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.12919.708171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.48115543
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9661538
X-RAY DIFFRACTIONr_chiral_restr0.2290.2472
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023941
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02732
LS refinement shellResolution: 2.65→2.718 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 61 -
Rwork0.372 1143 -
all-1204 -
obs--99.92 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.99440.60851.21896.82461.74514.3131-0.19040.06070.0368-0.08980.3460.4892-0.272-0.3936-0.15560.3192-0.01050.0720.34090.06670.0711-4.1917-19.409-4.0255
24.30830.3893-0.75654.231-1.50215.1745-0.12290.1381-0.10450.2210.1301-0.09480.819-0.4716-0.00710.3134-0.17590.0060.1922-0.03420.0127-1.3146-34.664-26.3011
33.0488-0.2503-0.27155.1749-1.59455.68420.0240.44440.0809-0.5189-0.2105-0.25710.3047-0.20090.18660.1329-0.03440.06250.35380.13650.11532.3769-20.0159-48.9584
43.3272-1.93440.03182.47270.53240.2574-0.43-0.4840.25480.36080.29860.2135-0.0484-0.07770.13140.4847-0.03790.0040.79650.14520.1641-15.0001-12.7423-22.9178
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 80
2X-RAY DIFFRACTION2A81 - 240
3X-RAY DIFFRACTION2A602
4X-RAY DIFFRACTION3A241 - 339
5X-RAY DIFFRACTION4A340 - 602

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