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- PDB-5uht: Structure of the Thermotoga maritima HK853-BeF3-RR468 complex at ... -

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Basic information

Entry
Database: PDB / ID: 5uht
TitleStructure of the Thermotoga maritima HK853-BeF3-RR468 complex at pH 5.0
Components
  • Response regulator
  • Sensor histidine kinase
KeywordsTRANSFERASE/SIGNALING PROTEIN / Two component system HK853 RR468 / TRANSFERASE-SIGNALING PROTEIN complex
Function / homology
Function and homology information


histidine phosphotransfer kinase activity / phosphorelay sensor kinase activity / histidine kinase / phosphorelay signal transduction system / nucleotide binding / metal ion binding / identical protein binding / plasma membrane
Similarity search - Function
Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain / : / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / Response regulator receiver domain ...Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain / : / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / Response regulator receiver domain / cheY-homologous receiver domain / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / 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-like ATPases / Histidine kinase/HSP90-like ATPase superfamily / Helix Hairpins / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Response regulator / histidine kinase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsLiu, Y. / Rose, J. / Jiang, L. / Zhou, P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM115355 United States
CitationJournal: Nat Commun / Year: 2017
Title: A pH-gated conformational switch regulates the phosphatase activity of bifunctional HisKA-family histidine kinases.
Authors: Liu, Y. / Rose, J. / Huang, S. / Hu, Y. / Wu, Q. / Wang, D. / Li, C. / Liu, M. / Zhou, P. / Jiang, L.
History
DepositionJan 12, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sensor histidine kinase
B: Response regulator
C: Sensor histidine kinase
D: Response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,86620
Polymers86,8454
Non-polymers2,02016
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11470 Å2
ΔGint-130 kcal/mol
Surface area30970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.970, 98.380, 72.050
Angle α, β, γ (deg.)90.00, 110.54, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Sensor histidine kinase


Mass: 29509.477 Da / Num. of mol.: 2 / Fragment: UNP residues 232-489
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM_0853
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9WZV7
#2: Protein Response regulator / RR468


Mass: 13913.255 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM_0468
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9WYT9

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Non-polymers , 5 types, 103 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.4 Å3/Da / Density % sol: 63.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 1:1 mixture of protein solution with mother liquor solution; Protein solution contains: 10 mg/mL HK853cp, 7.5 mg/mL RR468, 10 mM Tris (pH 8.0), 7 mM MgCl2, 5 mM BeCl2, 30 mM NaF, 4 mM AMPPNP. ...Details: 1:1 mixture of protein solution with mother liquor solution; Protein solution contains: 10 mg/mL HK853cp, 7.5 mg/mL RR468, 10 mM Tris (pH 8.0), 7 mM MgCl2, 5 mM BeCl2, 30 mM NaF, 4 mM AMPPNP. Mother liquor solution contains: 0.1 M citric acid (pH 4.0), 0.8 M ammonium sulfate. Adjust final pH to 5.0.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.68→49.19 Å / Num. obs: 32777 / % possible obs: 99.8 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 20.6
Reflection shellResolution: 2.68→2.75 Å / Rmerge(I) obs: 0.875 / % possible all: 87.5

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3dge

3dge


Resolution: 2.68→49.19 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 22.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2218 1660 5.07 %
Rwork0.1822 --
obs0.1842 32763 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.68→49.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5461 0 125 87 5673
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015718
X-RAY DIFFRACTIONf_angle_d0.7997749
X-RAY DIFFRACTIONf_dihedral_angle_d12.5583418
X-RAY DIFFRACTIONf_chiral_restr0.05907
X-RAY DIFFRACTIONf_plane_restr0.005978
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.68-2.75880.29861370.26022556X-RAY DIFFRACTION100
2.7588-2.84790.22781530.22242545X-RAY DIFFRACTION100
2.8479-2.94970.25941310.20352604X-RAY DIFFRACTION100
2.9497-3.06770.27231430.2152573X-RAY DIFFRACTION100
3.0677-3.20730.2551210.19932601X-RAY DIFFRACTION100
3.2073-3.37640.23531280.18032606X-RAY DIFFRACTION100
3.3764-3.58790.22731410.17112592X-RAY DIFFRACTION100
3.5879-3.86480.19081430.16962564X-RAY DIFFRACTION100
3.8648-4.25350.21041370.15922604X-RAY DIFFRACTION100
4.2535-4.86850.19951440.15062593X-RAY DIFFRACTION100
4.8685-6.1320.23031440.19772613X-RAY DIFFRACTION100
6.132-49.19830.2041380.18622652X-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)
12.29670.56160.98832.15530.98613.07160.027-0.1397-0.0055-0.03490.01320.24320.1172-0.4107-0.03410.2731-0.0140.00130.28410.06750.3368-24.818513.2365-7.4788
23.94230.9046-0.88694.158-0.8383.14980.3141-0.75220.120.5075-0.16120.01770.00340.3623-0.11510.5023-0.24570.02170.5929-0.00340.5135-36.925-5.8709-2.3351
32.5265-1.2548-0.46562.3563-0.10552.907-0.4245-1.47670.17220.67890.3984-0.0055-0.130.04160.06790.45710.1888-0.02780.6665-0.0680.3065-21.102425.090913.3062
41.7276-0.6848-0.1392.98860.49362.7824-0.5687-0.7023-0.28430.71430.23190.9978-0.2134-0.67130.31150.46670.19380.11550.646-0.00410.4661-35.70226.493811.4252
53.80790.6894-2.51692.7945-1.62362.1568-0.5079-0.92620.84571.0796-0.63020.9728-0.535-1.17450.70370.86920.14340.06151.0431-0.41680.7985-30.723737.845219.1342
61.6387-1.6168-0.98342.99531.03722.70.00180.14690.64840.1214-0.14470.3433-0.8368-0.54560.19580.47510.18540.01060.391-0.04420.5101-30.959631.93851.4224
73.5247-2.4257-2.72736.78872.89165.6351-0.1066-0.44771.3769-0.62260.27260.2817-0.90170.495-0.010.46830.0079-0.03260.417-0.15770.5796-17.16335.2363.6061
83.8303-0.77090.03672.1420.14841.91050.08310.44780.098-0.193700.228-0.2504-0.1078-0.05090.3177-0.0248-0.02750.26050.04820.2515-22.182516.1901-15.3728
93.094-0.39091.03374.0539-0.65633.80150.13540.30510.1236-0.1879-0.0889-0.37340.36620.5075-0.08030.54070.1787-0.02540.56070.11480.438-27.716334.3188-26.6867
103.7239-0.2475-0.91463.41110.30983.24860.0950.21270.073-0.3596-0.0693-0.29060.08840.5266-0.02450.69780.22440.02460.6040.12160.4199-31.080136.8756-30.8806
111.84940.4085-0.67621.13860.15843.1876-0.01120.5621-0.268-0.02190.1599-0.35-0.11590.9138-0.22740.3212-0.10180.05290.5552-0.16020.4434-5.73745.7234-23.0762
123.8027-1.85723.2014.3443-2.76394.7756-0.57180.60330.1007-0.45710.7543-0.4576-0.09590.7668-0.07690.485-0.22030.15630.9838-0.10310.4923-4.52216.5784-29.069
131.56961.4142-0.3732.9071.73092.69880.00310.84260.3988-0.28880.1065-0.3294-0.390.3215-0.09460.837-0.55720.50751.3165-0.5554-0.2189-7.42435.3426-39.0076
142.05960.2551-1.27160.77161.01052.7196-0.12160.98970.1559-0.23840.8865-1.2075-0.22351.1597-0.37250.412-0.13950.05871.0956-0.3940.7236-4.1944-0.8475-33.1714
151.93120.2935-1.13121.5186-0.82962.0516-0.27821.4504-0.4024-0.84680.60640.0295-0.34810.3313-0.0760.6521-0.1864-0.00270.8744-0.21710.4541-17.10751.2193-37.2287
161.5957-0.30070.06163.36040.20252.7749-0.45031.3865-1.18740.0036-0.01510.33290.87620.24630.34010.49140.00310.03170.735-0.25710.5258-12.8851-4.1336-32.484
174.73160.67020.98765.6808-2.64921.6116-0.2592-0.0117-0.43450.1918-0.3119-0.0742-0.1914-0.75210.29990.5787-0.0795-0.05880.5822-0.25240.5095-25.6438-5.6891-29.7621
180.740.8844-0.15972.96032.33234.58630.6373-0.0305-0.7491-0.16530.1919-0.73910.41560.4828-0.69740.3878-0.025-0.03380.3603-0.190.5194-17.1321-2.3608-23.3334
192.2091-1.132-1.03687.31961.38875.5720.19080.4587-1.23690.0130.44020.27551.01180.6536-0.56520.42640.1159-0.17580.4818-0.23470.7075-8.4181-5.5079-18.4806
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 245 through 316 )
2X-RAY DIFFRACTION2chain 'A' and (resid 317 through 479 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 52 )
4X-RAY DIFFRACTION4chain 'B' and (resid 54 through 68 )
5X-RAY DIFFRACTION5chain 'B' and (resid 69 through 78 )
6X-RAY DIFFRACTION6chain 'B' and (resid 79 through 108 )
7X-RAY DIFFRACTION7chain 'B' and (resid 109 through 121 )
8X-RAY DIFFRACTION8chain 'C' and (resid 245 through 316 )
9X-RAY DIFFRACTION9chain 'C' and (resid 317 through 465 )
10X-RAY DIFFRACTION10chain 'C' and (resid 466 through 480 )
11X-RAY DIFFRACTION11chain 'D' and (resid 1 through 25 )
12X-RAY DIFFRACTION12chain 'D' and (resid 26 through 34 )
13X-RAY DIFFRACTION13chain 'D' and (resid 35 through 42 )
14X-RAY DIFFRACTION14chain 'D' and (resid 43 through 52 )
15X-RAY DIFFRACTION15chain 'D' and (resid 54 through 70 )
16X-RAY DIFFRACTION16chain 'D' and (resid 71 through 87 )
17X-RAY DIFFRACTION17chain 'D' and (resid 88 through 96 )
18X-RAY DIFFRACTION18chain 'D' and (resid 97 through 108 )
19X-RAY DIFFRACTION19chain 'D' and (resid 109 through 121 )

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