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- PDB-5iuk: Crystal structure of the DesK-DesR complex in the phosphotransfer... -

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Basic information

Entry
Database: PDB / ID: 5iuk
TitleCrystal structure of the DesK-DesR complex in the phosphotransfer state with high Mg2+ (150 mM)
Components
  • Sensor histidine kinase DesK
  • Transcriptional regulatory protein DesR
KeywordsTRANSFERASE/GENE REGULATION / Two-component regulatory system / Kinase / Response regulator / Phosphotransfer complex / Phosphotransfer / TRANSFERASE / TRANSFERASE-GENE REGULATION complex
Function / homology
Function and homology information


histidine kinase / phosphorelay signal transduction system / phosphoprotein phosphatase activity / phosphorelay sensor kinase activity / protein dimerization activity / protein kinase activity / regulation of DNA-templated transcription / DNA binding / ATP binding / identical protein binding ...histidine kinase / phosphorelay signal transduction system / phosphoprotein phosphatase activity / phosphorelay sensor kinase activity / protein dimerization activity / protein kinase activity / regulation of DNA-templated transcription / DNA binding / ATP binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Signal transduction histidine kinase, subgroup 3, dimerisation and phosphoacceptor domain / Histidine kinase / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain ...Signal transduction histidine kinase, subgroup 3, dimerisation and phosphoacceptor domain / Histidine kinase / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Winged helix-like DNA-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / : / Transcriptional regulatory protein DesR / Sensor histidine kinase DesK
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsTrajtenberg, F. / Imelio, J.A. / Larrieux, N. / Buschiazzo, A.
CitationJournal: Elife / Year: 2016
Title: Regulation of signaling directionality revealed by 3D snapshots of a kinase:regulator complex in action.
Authors: Trajtenberg, F. / Imelio, J.A. / Machado, M.R. / Larrieux, N. / Marti, M.A. / Obal, G. / Mechaly, A.E. / Buschiazzo, A.
History
DepositionMar 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2016Group: Database references
Revision 1.2Jan 4, 2017Group: Database references
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sensor histidine kinase DesK
B: Sensor histidine kinase DesK
D: Sensor histidine kinase DesK
E: Sensor histidine kinase DesK
C: Transcriptional regulatory protein DesR
F: Transcriptional regulatory protein DesR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,26417
Polymers130,0436
Non-polymers2,22111
Water1629
1
A: Sensor histidine kinase DesK
B: Sensor histidine kinase DesK
C: Transcriptional regulatory protein DesR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1449
Polymers65,0223
Non-polymers1,1226
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8810 Å2
ΔGint-80 kcal/mol
Surface area29590 Å2
MethodPISA
2
D: Sensor histidine kinase DesK
E: Sensor histidine kinase DesK
F: Transcriptional regulatory protein DesR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1208
Polymers65,0223
Non-polymers1,0985
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9030 Å2
ΔGint-69 kcal/mol
Surface area29240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.930, 115.610, 91.590
Angle α, β, γ (deg.)90.000, 116.710, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 6 molecules ABDECF

#1: Protein
Sensor histidine kinase DesK


Mass: 24956.590 Da / Num. of mol.: 4 / Fragment: Fragment: entire cytoplasmic region / Mutation: H188E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: desK, yocF, BSU19190 / Plasmid: pACYC-Duet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O34757, histidine kinase
#2: Protein Transcriptional regulatory protein DesR


Mass: 15108.367 Da / Num. of mol.: 2 / Fragment: Receiver domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: desR, yocG, BSU19200 / Plasmid: pACYC-Duet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O34723

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Non-polymers , 4 types, 20 molecules

#3: Chemical
ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 3.2 Å3/Da / Density % sol: 61.54 % / Mosaicity: 0.16 °
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG3350, tri-potassium citrate, vapor diffusion, hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 14, 2016 / Details: Kirkpatrick-Baez pair of bi-morph mirrors
RadiationMonochromator: channel cut cryogenically cooled monochromator crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.9→66.78 Å / Num. obs: 36132 / % possible obs: 99.1 % / Redundancy: 5.8 % / Biso Wilson estimate: 95.89 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 12.5
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 6 % / Rmerge(I) obs: 1.471 / % possible all: 99.2

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Processing

Software
NameVersionClassification
BUSTER-TNT2.10.2refinement
XDSJun 17, 2015data scaling
Aimless0.5.17data scaling
PHASER2.5.7phasing
Coot0.8.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→39.27 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.927 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 21.829 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.289 / SU Rfree Blow DPI: 0.335 / SU Rfree Cruickshank DPI: 0.348
RfactorNum. reflection% reflectionSelection details
Rfree0.239 1720 4.86 %RANDOM
Rwork0.195 ---
obs0.198 35374 97.3 %-
Displacement parametersBiso max: 215.65 Å2 / Biso mean: 102.47 Å2 / Biso min: 43.77 Å2
Baniso -1Baniso -2Baniso -3
1-2.7509 Å20 Å22.2546 Å2
2---10.9 Å20 Å2
3---8.1491 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: final / Resolution: 2.9→39.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8702 0 131 9 8842
Biso mean--129.58 78.36 -
Num. residues----1100
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3437SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes286HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1270HARMONIC5
X-RAY DIFFRACTIONt_it8904HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1192SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance27HARMONIC1
X-RAY DIFFRACTIONt_utility_angle26HARMONIC1
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact10082SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d8904HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg11965HARMONIC21.25
X-RAY DIFFRACTIONt_omega_torsion3.41
X-RAY DIFFRACTIONt_other_torsion19.61
LS refinement shellResolution: 2.9→2.98 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.326 143 5.44 %
Rwork0.274 2486 -
all-2629 -
obs--89.12 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.9610.00480.56180.5593-0.92897.3046-0.03330.04440.14950.01710.0372-0.0041-0.120.28-0.004-0.2447-0.0718-0.0720.23310.1229-0.2516-15.68914.807-9.22
24.6841-0.87891.08837.37730.07286.03820.0071-0.06780.57790.43730.03580.3417-0.5105-0.6434-0.0429-0.27130.0496-0.02420.3040.1869-0.3366-42.97721.748-28.473
36.0055-2.91542.40827.6911-0.68115.3354-0.17330.55750.3847-0.4769-0.1972-0.2631-0.09370.10290.3705-0.1601-0.1899-0.14130.3040.0746-0.31057.61234.355-20.098
43.89660.6721.90480.73780.19792.30980.057-0.2252-0.14310.1701-0.0924-0.12420.120.13340.0354-0.2325-0.1067-0.02190.2945-0.0065-0.3319-66.05218.34923.496
53.9936-0.52791.10356.70870.1716.02110.04520.4865-0.4066-0.4080.0331-0.20450.64130.2441-0.0783-0.2083-0.0303-0.0710.3021-0.1478-0.3996-69.30310.768-9.431
65.8098-2.0861.4518.31552.20847.72140.16730.2122-0.3434-0.1502-0.03650.45070.7451-0.5025-0.1308-0.1677-0.0949-0.11890.3040.1224-0.3698-86.509-1.33337.413
76.07341.60141.42725.9568-1.04235.83380.0020.0686-0.5565-0.0451-0.02230.36890.532-0.36580.0203-0.3037-0.05050.01340.18780.0299-0.239-34.6361.3195.148
85.62.0609-0.23735.6091-1.48187.0557-0.00680.16980.126-0.3090.0223-0.5216-0.64570.573-0.0155-0.0782-0.14410.19430.086-0.01-0.1656-43.46430.34114.042
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|155 - A|242 B|154 - B|239 }A155 - 242
2X-RAY DIFFRACTION1{ A|155 - A|242 B|154 - B|239 }B154 - 239
3X-RAY DIFFRACTION2{ A|245 - A|368 A|401 - A|402 }A245 - 368
4X-RAY DIFFRACTION2{ A|245 - A|368 A|401 - A|402 }A401 - 402
5X-RAY DIFFRACTION3{ B|245 - B|367 B|401 - B|402 }B245 - 367
6X-RAY DIFFRACTION3{ B|245 - B|367 B|401 - B|402 }B401 - 402
7X-RAY DIFFRACTION4{ E|154 - E|239 D|155 - D|242 }E154 - 239
8X-RAY DIFFRACTION4{ E|154 - E|239 D|155 - D|242 }D155 - 242
9X-RAY DIFFRACTION5{ D|245 - D|369 D|401 - D|402 }D245 - 369
10X-RAY DIFFRACTION5{ D|245 - D|369 D|401 - D|402 }D401 - 402
11X-RAY DIFFRACTION6{ E|245 - E|367 E|401 - E|402 }E245 - 367
12X-RAY DIFFRACTION6{ E|245 - E|367 E|401 - E|402 }E401 - 402
13X-RAY DIFFRACTION7{ C|0 - C|131 }C0 - 131
14X-RAY DIFFRACTION8{ F|0 - F|131 }F0 - 131

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