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- PDB-1p0z: Sensor Kinase CitA binding domain -

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Basic information

Entry
Database: PDB / ID: 1p0z
TitleSensor Kinase CitA binding domain
ComponentsSensor kinase citA
KeywordsTRANSFERASE / Kinase
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity / ATP binding / plasma membrane
Similarity search - Function
Single cache domain 3 / Single cache domain 3 / Signal transduction histidine kinase, sporulation regulator SpoOB / Periplasmic sensor-like domain superfamily / PAS domain / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Beta-Lactamase / PAS domain ...Single cache domain 3 / Single cache domain 3 / Signal transduction histidine kinase, sporulation regulator SpoOB / Periplasmic sensor-like domain superfamily / PAS domain / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Beta-Lactamase / PAS domain / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain superfamily / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRATE ANION / Chem-MO7 / MO(VI)(=O)(OH)2 CLUSTER / Sensor histidine kinase CitA
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsReinelt, S. / Hofmann, E. / Gerharz, T. / Bott, M. / Madden, D.R.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: The structure of the periplasmic ligand-binding domain of the sensor kinase CitA reveals the first extracellular PAS domain.
Authors: Reinelt, S. / Hofmann, E. / Gerharz, T. / Bott, M. / Madden, D.R.
History
DepositionApr 11, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 9, 2014Group: Non-polymer description
Revision 1.4Sep 10, 2014Group: Database references
Revision 1.5Feb 14, 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_ref_seq_dif / struct_sheet / 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.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_ref_seq_dif.details / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT ...BIOMOLECULE: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 10CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). THE MONOMER IS LIGAND-BINDING COMPETENT. GEL FILTRATION ANALYSIS REVEALS WEAK DIMERIZATION IN SOLUTION WHICH MAY REPRESENT THE OLIGOMERIZATION STATE OF THE RECEPTOR IN VIVO. TWO CANDIDATE DIMER INTERFACES ARE DETECTED IN THE CRYSTAL, INVOLVING EITHER CHAINS E AND G OR CHAINS G AND J.
Remark 650HELIX determination method: Author determined
Remark 700SHEET determination method: Author determined

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sensor kinase citA
B: Sensor kinase citA
C: Sensor kinase citA
D: Sensor kinase citA
E: Sensor kinase citA
F: Sensor kinase citA
G: Sensor kinase citA
H: Sensor kinase citA
I: Sensor kinase citA
J: Sensor kinase citA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,28850
Polymers143,15210
Non-polymers14,13640
Water28,3381573
1
A: Sensor kinase citA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7295
Polymers14,3151
Non-polymers1,4144
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sensor kinase citA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7295
Polymers14,3151
Non-polymers1,4144
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Sensor kinase citA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7295
Polymers14,3151
Non-polymers1,4144
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Sensor kinase citA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7295
Polymers14,3151
Non-polymers1,4144
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Sensor kinase citA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7295
Polymers14,3151
Non-polymers1,4144
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Sensor kinase citA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7295
Polymers14,3151
Non-polymers1,4144
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Sensor kinase citA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7295
Polymers14,3151
Non-polymers1,4144
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Sensor kinase citA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7295
Polymers14,3151
Non-polymers1,4144
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Sensor kinase citA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7295
Polymers14,3151
Non-polymers1,4144
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: Sensor kinase citA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7295
Polymers14,3151
Non-polymers1,4144
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.613, 84.333, 97.710
Angle α, β, γ (deg.)112.83, 107.36, 93.74
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 10 molecules ABCDEFGHIJ

#1: Protein
Sensor kinase citA


Mass: 14315.185 Da / Num. of mol.: 10 / Fragment: CitA binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: CITA / Production host: Escherichia coli (E. coli) / References: UniProt: P52687, histidine kinase

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Non-polymers , 5 types, 1613 molecules

#2: Chemical
ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-MO7 / bis(mu4-oxo)-bis(mu3-oxo)-octakis(mu2-oxo)-dodecaoxo-heptamolybdenum (VI) / HEPTAMOLYBDATE [Mo(VI)7O24]6-


Mass: 1055.566 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mo7O24
#5: Chemical
ChemComp-OMO / MO(VI)(=O)(OH)2 CLUSTER


Mass: 145.954 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: H2MoO3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1573 / 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: 2.48 Å3/Da / Density % sol: 50.05 %
Crystal growTemperature: 289 K / pH: 6
Details: HANGING DROP, VAPOUR DIFFUSION, RESERVOIR: 100MM NA2MOO4, 100MM MES, PH 6.0, 8% PEG4000, 2.5% GLYCEROL, PROTEIN SOLUTION: 10MM NACL, 10MM TRIS, PH 8.0, 1MM NA-CITRATE, 16MG/ML PROTEIN CONC. ...Details: HANGING DROP, VAPOUR DIFFUSION, RESERVOIR: 100MM NA2MOO4, 100MM MES, PH 6.0, 8% PEG4000, 2.5% GLYCEROL, PROTEIN SOLUTION: 10MM NACL, 10MM TRIS, PH 8.0, 1MM NA-CITRATE, 16MG/ML PROTEIN CONC. MIXING RATIO 1:1., temperature 289K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
1100 mM1reservoirNa2MoO4
2100 mMMES1reservoirpH6.0
38 %(w/v)PEG40001reservoir
42.5 %(v/v)glycerol1reservoiror 14%PEG4000 and 15%glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9393
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: May 9, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 1.6→38.03 Å / Num. obs: 214649 / % possible obs: 95.9 % / Redundancy: 8.7 % / Biso Wilson estimate: 23.6 Å2 / Rsym value: 0.103 / Net I/σ(I): 11.88
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 8.6 % / Mean I/σ(I) obs: 4.24 / Rsym value: 0.646 / % possible all: 92.8
Reflection
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 38 Å / % possible obs: 95.8 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.103

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Processing

Software
NameVersionClassification
CNS1.1refinement
XDSdata reduction
XSCALEdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→38.03 Å / Rfactor Rfree error: 0.002 / Data cutoff high rms absF: 1633341.02 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
Details: The high-res bin for the R_work is different from that for R_free. The bin for R_work is 1.7-1.6 A. The bin for R_free is 1.71 to 1.72. The RMS DEVIATIONS in reamrk 3 are the RMS DEVIATIONS ...Details: The high-res bin for the R_work is different from that for R_free. The bin for R_work is 1.7-1.6 A. The bin for R_free is 1.71 to 1.72. The RMS DEVIATIONS in reamrk 3 are the RMS DEVIATIONS FOR ALL ATOMS. The RMS DEVIATIONS FROM IDEAL VALUES FOR PROTEIN ATOMS are 0.014A for BOND LENGTHS, 1.70 degree for BOND ANGLES, 23.40 degree for DIHEDRAL ANGLES, 1.07 degree for IMPROPER ANGLES.
RfactorNum. reflection% reflectionSelection details
Rfree0.19 6704 3.1 %SHELLS
Rwork0.168 ---
obs0.168 214649 95.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.47 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 28.2 Å2
Baniso -1Baniso -2Baniso -3
1-5.33 Å2-3.27 Å20.17 Å2
2---0.99 Å2-1.09 Å2
3----4.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.6→38.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9980 0 490 1573 12043
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.019
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.15
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.091.5
X-RAY DIFFRACTIONc_mcangle_it1.682
X-RAY DIFFRACTIONc_scbond_it1.752
X-RAY DIFFRACTIONc_scangle_it2.592.5
Refine LS restraints NCSNCS model details: RESTRAINED / Weight Biso : 2 / Weight position: 300
LS refinement shellResolution: 1.6→1.7 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.228 --
Rwork0.242 34591 -
obs--92.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3ION.PARAMWATER.TOP
X-RAY DIFFRACTION4177-LIGANDS.PARION.TOP
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 38 Å / Rfactor Rfree: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.15

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