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- PDB-1id0: CRYSTAL STRUCTURE OF THE NUCLEOTIDE BOND CONFORMATION OF PHOQ KIN... -

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Basic information

Entry
Database: PDB / ID: 1id0
TitleCRYSTAL STRUCTURE OF THE NUCLEOTIDE BOND CONFORMATION OF PHOQ KINASE DOMAIN
ComponentsPHOQ HISTIDINE KINASE
KeywordsTRANSFERASE / Histidine kinase / PhoQ/PhoP / signal transduction
Function / homology
Function and homology information


osmosensory signaling via phosphorelay pathway / cellular response to magnesium starvation / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / histidine kinase / phosphorelay sensor kinase activity / phosphoprotein phosphatase activity / phosphorelay signal transduction system / kinase activity / signal transduction / ATP binding ...osmosensory signaling via phosphorelay pathway / cellular response to magnesium starvation / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / histidine kinase / phosphorelay sensor kinase activity / phosphoprotein phosphatase activity / phosphorelay signal transduction system / kinase activity / signal transduction / ATP binding / identical protein binding / metal ion binding / plasma membrane
Similarity search - Function
PhoQ Sensor / PhoQ Sensor superfamily / PhoQ Sensor / HAMP domain profile. / HAMP 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 ...PhoQ Sensor / PhoQ Sensor superfamily / PhoQ Sensor / HAMP domain profile. / HAMP 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Sensor protein PhoQ
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsMarina, A. / Mott, C. / Auyzenberg, A. / Waldburger, C.D. / Hendrickson, W.A.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: Structural and mutational analysis of the PhoQ histidine kinase catalytic domain. Insight into the reaction mechanism.
Authors: Marina, A. / Mott, C. / Auyzenberg, A. / Hendrickson, W.A. / Waldburger, C.D.
History
DepositionApr 2, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 1, 2017Group: Structure summary
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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.ptnr3_auth_comp_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.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_conn.ptnr2_label_seq_id / _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: PHOQ HISTIDINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3763
Polymers16,8451
Non-polymers5312
Water3,405189
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.503, 45.004, 71.764
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PHOQ HISTIDINE KINASE / SENSOR PROTEIN PHOQ


Mass: 16845.008 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PAED4QKD / Production host: Escherichia coli (E. coli) / References: UniProt: P23837, EC: 2.7.1.37
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 2.08 Å3/Da / Density % sol: 40.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: a cacodylate, PEG 1500, Mg acetate, pH 6.5, VAPORDIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
210 mMTris-HCl1droppH8.5
3100 mM1dropNaCl
4100 mMcacodylate1reservoirpH6.5
520-24 %PEG15001reservoir
6100-200 mMmagnesium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 17, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.6→22.5 Å / Num. all: 26236 / Num. obs: 19159 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.4 % / Biso Wilson estimate: 18.1 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 32.5
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.186 / % possible all: 99.9
Reflection
*PLUS
Redundancy: 10.5 % / Num. measured all: 34398

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Processing

Software
NameVersionClassification
MADSYSphasing
MLPHAREphasing
DMmodel building
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
DMphasing
RefinementMethod to determine structure: MAD / Resolution: 1.6→22.5 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 956397.32 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: engh & huber
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1400 7.3 %RANDOM
Rwork0.199 ---
obs-19159 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.29 Å2 / ksol: 0.362 e/Å3
Displacement parametersBiso mean: 25.1 Å2
Baniso -1Baniso -2Baniso -3
1--3.39 Å20 Å20 Å2
2---1.57 Å20 Å2
3---4.96 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→22.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1137 0 32 189 1358
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_improper_angle_d5.2
LS refinement shellResolution: 1.6→1.64 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.299 90 7.2 %
Rwork0.249 1156 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ANP_MUTL.PARANP_MUTL.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 7.5 % / Rfactor obs: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 25.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg5.2
LS refinement shell
*PLUS
Rfactor Rfree: 0.299 / % reflection Rfree: 7.2 % / Rfactor Rwork: 0.249

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