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- PDB-5lfk: Crystal structure of CpxAHDC (hemiphosphorylated form) -

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Basic information

Entry
Database: PDB / ID: 5lfk
TitleCrystal structure of CpxAHDC (hemiphosphorylated form)
Components(Sensor histidine kinase CpxA) x 2
KeywordsTRANSFERASE / Two-Componet Systems / Histidine Kinase
Function / homology
Function and homology information


cell adhesion involved in biofilm formation / cellular response to cell envelope stress / histidine kinase / phosphoprotein phosphatase activity / phosphorelay sensor kinase activity / response to radiation / signal transduction / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
Two-component sensor protein CpxA, periplasmic domain / Two-component sensor protein CpxA, periplasmic domain superfamily / Two-component sensor protein CpxA, periplasmic domain / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain ...Two-component sensor protein CpxA, periplasmic domain / Two-component sensor protein CpxA, periplasmic domain superfamily / Two-component sensor protein CpxA, periplasmic domain / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP 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-, 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
ADENOSINE-5'-TRIPHOSPHATE / Sensor histidine kinase CpxA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.094 Å
AuthorsMechaly, A.E. / Alzari, P.M.
CitationJournal: Structure / Year: 2017
Title: Structural Coupling between Autokinase and Phosphotransferase Reactions in a Bacterial Histidine Kinase.
Authors: Mechaly, A.E. / Soto Diaz, S. / Sassoon, N. / Buschiazzo, A. / Betton, J.M. / Alzari, P.M.
History
DepositionJul 1, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / exptl_crystal / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _exptl_crystal.density_Matthews / _exptl_crystal.density_percent_sol / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sensor histidine kinase CpxA
B: Sensor histidine kinase CpxA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,34712
Polymers66,7082
Non-polymers1,63910
Water00
1
A: Sensor histidine kinase CpxA
B: Sensor histidine kinase CpxA
hetero molecules

A: Sensor histidine kinase CpxA
B: Sensor histidine kinase CpxA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,69424
Polymers133,4164
Non-polymers3,27920
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_557x,x-y,-z+13/61
Buried area22110 Å2
ΔGint-281 kcal/mol
Surface area41290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.734, 145.734, 225.191
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
11B-503-

SO4

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Components

#1: Protein Sensor histidine kinase CpxA


Mass: 33314.422 Da / Num. of mol.: 1 / Fragment: UNP residues 188-457 / Mutation: M228V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cpxA, ecfB, eup, ssd, b3911, JW3882 / Production host: Escherichia coli (E. coli) / Strain (production host): B5 / References: UniProt: P0AE82, histidine kinase
#2: Protein Sensor histidine kinase CpxA


Mass: 33393.395 Da / Num. of mol.: 1 / Fragment: UNP residues 188-457
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cpxA, ecfB, eup, ssd, b3911, JW3882 / Production host: Escherichia coli (E. coli) / Strain (production host): B5 / References: UniProt: P0AE82, histidine kinase
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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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: 5.17 Å3/Da / Density % sol: 76.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 100 mM Tris (pH 8.5), 1.5 M ammonium sulphate and 12 % v/v glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97934 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 3.09→48.3 Å / Num. obs: 26453 / % possible obs: 99.6 % / Redundancy: 11.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.094 / Rsym value: 0.103 / Net I/σ(I): 9.4
Reflection shellResolution: 3.09→3.31 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.774 / Mean I/σ(I) obs: 1.8 / CC1/2: 0.921 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BIW

4biw


Resolution: 3.094→47.703 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 0.96 / Phase error: 26.77
RfactorNum. reflection% reflection
Rfree0.2201 2469 5.08 %
Rwork0.1947 --
obs0.1961 26377 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.094→47.703 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3769 0 94 0 3863
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0183926
X-RAY DIFFRACTIONf_angle_d1.225334
X-RAY DIFFRACTIONf_dihedral_angle_d14.4962364
X-RAY DIFFRACTIONf_chiral_restr0.057590
X-RAY DIFFRACTIONf_plane_restr0.006689
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0945-3.1540.41481590.40982386X-RAY DIFFRACTION94
3.154-3.21840.34461360.37982572X-RAY DIFFRACTION100
3.2184-3.28830.39831310.35132580X-RAY DIFFRACTION100
3.2883-3.36480.36561420.32082535X-RAY DIFFRACTION100
3.3648-3.44890.32631230.2932598X-RAY DIFFRACTION100
3.4489-3.54210.26431310.25592584X-RAY DIFFRACTION100
3.5421-3.64630.28541360.24822581X-RAY DIFFRACTION100
3.6463-3.7640.34331400.23452558X-RAY DIFFRACTION100
3.764-3.89840.23621250.21662582X-RAY DIFFRACTION100
3.8984-4.05450.2141530.19712584X-RAY DIFFRACTION100
4.0545-4.23890.20581550.18942532X-RAY DIFFRACTION100
4.2389-4.46220.18311340.1442576X-RAY DIFFRACTION100
4.4622-4.74150.13851380.12852563X-RAY DIFFRACTION100
4.7415-5.10720.16831300.14352575X-RAY DIFFRACTION100
5.1072-5.62050.22131480.16892580X-RAY DIFFRACTION100
5.6205-6.43210.23531350.18562568X-RAY DIFFRACTION100
6.4321-8.09730.16181300.16732591X-RAY DIFFRACTION100
8.0973-47.70830.16351230.15042590X-RAY DIFFRACTION100
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)
13.5331-1.4665-0.8053.30120.5071.85380.09740.5834-0.3385-0.3749-0.20910.6922-0.1845-0.16920.09390.481-0.0606-0.07330.7323-0.04781.1189115.176575.089230.8568
23.9923-0.1302-0.92214.79940.1263.28750.25520.36920.7867-0.4805-0.36870.265-0.30250.00020.13580.49410.01430.1010.7720.04930.9334141.562874.5786220.0353
37.399-2.1471-1.60232.11313.42885.9737-0.2841-0.25161.0644-0.07820.10540.0198-0.4587-0.17310.15910.4752-0.06030.04390.6774-0.02511.1169136.316376.5457231.3179
45.963-2.9646-1.08985.14691.19261.8185-0.1350.25010.19050.1213-0.121-0.3316-0.0814-0.11470.21010.4677-0.05290.03490.6775-0.00380.9973117.896673.7384239.8758
57.05112.57472.00321.61890.97312.91150.07740.0427-0.08490.16320.0383-0.2548-0.0770.1819-0.05630.46910.0768-0.10690.7832-0.05050.923493.99270.5884228.5034
66.20871.04730.22547.2179-3.57238.577-0.10440.7881-0.2195-0.89890.3023-0.36780.02790.6999-0.16110.5462-0.0439-0.04350.8741-0.24940.833199.970168.5953216.2854
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 213 through 298 )
2X-RAY DIFFRACTION2chain 'A' and (resid 299 through 394 )
3X-RAY DIFFRACTION3chain 'A' and (resid 395 through 455 )
4X-RAY DIFFRACTION4chain 'B' and (resid 216 through 294 )
5X-RAY DIFFRACTION5chain 'B' and (resid 295 through 386 )
6X-RAY DIFFRACTION6chain 'B' and (resid 387 through 455 )

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