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- PDB-6mi6: STRUCTURE OF CHEA DOMAIN P4 IN COMPLEX WITH AN ADP ANALOG -

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Basic information

Entry
Database: PDB / ID: 6mi6
TitleSTRUCTURE OF CHEA DOMAIN P4 IN COMPLEX WITH AN ADP ANALOG
ComponentsChemotaxis protein CheA
KeywordsSIGNALING PROTEIN / bacterial chemotaxis / histidine kinase / Thermotoga maritima
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity / chemotaxis / protein domain specific binding / ATP binding / cytoplasm
Similarity search - Function
Chemotaxis protein CheA, P2 response regulator-binding domain superfamily / Chemotaxis protein CheA, P2 response regulator-binding / P2 response regulator binding domain / Histidine kinase CheA-like, homodimeric domain / CheY-binding domain of CheA / Histidine kinase CheA-like, homodimeric domain superfamily / Signal transducing histidine kinase, homodimeric domain / Signal transducing histidine kinase, homodimeric domain / CheW-like domain profile. / CheW-like domain ...Chemotaxis protein CheA, P2 response regulator-binding domain superfamily / Chemotaxis protein CheA, P2 response regulator-binding / P2 response regulator binding domain / Histidine kinase CheA-like, homodimeric domain / CheY-binding domain of CheA / Histidine kinase CheA-like, homodimeric domain superfamily / Signal transducing histidine kinase, homodimeric domain / Signal transducing histidine kinase, homodimeric domain / CheW-like domain profile. / CheW-like domain / CheW-like domain superfamily / CheW-like domain / Two component signalling adaptor domain / Histidine Phosphotransfer domain / Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. / Signal transduction histidine kinase, phosphotransfer (Hpt) domain / HPT domain superfamily / 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'-DIPHOSPHATE / Chem-JSJ / Chemotaxis protein CheA
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.95 Å
AuthorsCrane, B.R. / Muok, A.R. / Chua, T.K. / Le, H.
CitationJournal: Appl.Magn.Reson. / Year: 2018
Title: Nucleotide Spin Labeling for ESR Spectroscopy of ATP-Binding Proteins.
Authors: Muok, A.R. / Chua, T.K. / Le, H. / Crane, B.R.
History
DepositionSep 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chemotaxis protein CheA
B: Chemotaxis protein CheA
C: Chemotaxis protein CheA
D: Chemotaxis protein CheA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,36112
Polymers83,8654
Non-polymers2,4968
Water00
1
A: Chemotaxis protein CheA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7874
Polymers20,9661
Non-polymers8213
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Chemotaxis protein CheA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5952
Polymers20,9661
Non-polymers6291
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Chemotaxis protein CheA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5864
Polymers20,9661
Non-polymers6193
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Chemotaxis protein CheA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3932
Polymers20,9661
Non-polymers4271
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.703, 75.145, 86.580
Angle α, β, γ (deg.)90.00, 90.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Chemotaxis protein CheA


Mass: 20966.240 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: cheA, TM_0702 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q56310, histidine kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: SO4
#3: Chemical ChemComp-JSJ / 5'-O-[(S)-hydroxy{[(S)-hydroxy{[(1-hydroxy-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl]disulfanyl}phosphoryl]oxy}phosphoryl]adenosine


Mass: 628.553 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C19H30N6O10P2S2
#4: 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

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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: 3.22 Å3/Da / Density % sol: 61.82 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 50 mM Citrate pH 5.5, 2 M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9722 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9722 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 25447 / % possible obs: 93.41 % / Redundancy: 3.2 % / CC1/2: 0.459 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.04 / Rrim(I) all: 0.071 / Χ2: 0.559 / Net I/av σ(I): 7.7 / Net I/σ(I): 5.7
Reflection shellResolution: 2.95→3.053 Å / Redundancy: 2 % / Num. unique obs: 1692 / % possible all: 99.27

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data collection
PHASERphasing
Cootmodel building
RefinementResolution: 2.95→10 Å / Cross valid method: THROUGHOUT / σ(F): 53.28 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2977 1727 8.09 %
Rwork0.2325 --
obs0.2398 21358 96.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.95→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5535 0 152 0 5687
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0155760
X-RAY DIFFRACTIONf_angle_d1.7717795
X-RAY DIFFRACTIONf_dihedral_angle_d9.8073504
X-RAY DIFFRACTIONf_chiral_restr0.082901
X-RAY DIFFRACTIONf_plane_restr0.012995
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)
13.58-1.243-0.09027.7141-1.41822.2624-0.0067-0.4621-0.03770.52010.1464-0.456-0.06690.145-0.03540.4863-0.0811-0.04810.4929-0.07120.49475.92383.914556.6242
27.4377-0.8899-0.01471.9521-0.28648.9021-0.6864-0.36750.71120.7757-0.1248-1.5076-0.75990.42890.48270.64250.0248-0.26480.56960.11620.842419.452123.899854.0808
32.7986-1.3043-0.5511.64280.83531.91530.2145-0.20380.88450.5093-0.4718-1.3489-0.25680.25230.27480.6029-0.3845-0.22630.72710.16091.023516.52369.051253.7355
49.02244.36254.98464.02912.95098.56050.16820.40270.7358-0.6986-0.52580.9646-0.17370.26090.350.68250.14520.05070.4851-0.00680.50563.726330.327227.2021
58.64572.41622.47543.71534.5295.6858-0.28481.21830.6077-1.2938-0.0746-1.2766-0.30160.64580.66710.79680.19330.35520.87690.37110.791413.168329.003927.6743
61.84722.31420.04026.4318-3.2664.34950.11791.6462-3.5974-3.27550.54911.31670.5835-0.9542-0.61750.9965-0.1086-0.18610.9039-0.0441.3805-3.35779.729928.1089
75.36354.02086.52394.33124.55838.07611.5133-1.6655-0.41460.28240.0203-0.9816-0.4101-0.3507-0.4067-0.21141.2466-0.084-0.20930.29950.80865.465124.872437.102
80.78520.78830.9029.3733-0.56093.11160.66350.5611-1.4775-1.5525-0.8592-0.51590.54370.41960.16480.8297-0.0390.16240.6185-0.05930.839614.55274.457731.7872
98.78937.22964.18576.2582.08468.10981.9326-1.2755-1.0447-0.9579-1.0369-1.68241.93280.1298-1.07410.6980.57840.3881.29150.51371.149725.29952.243438.474
108.2028-0.3806-5.19836.10694.15649.2472-0.6096-0.059-0.9484-0.59480.5602-0.13450.83570.93710.64170.7889-0.00170.49940.40090.1271.336119.603610.039329.2689
117.95632.71783.15196.25112.49428.57280.58390.1431-1.15380.03191.2170.78550.129-0.4531-1.13430.73140.06110.09530.58030.22191.067620.679220.138223.6897
122.02198.3306-4.40916.9307-4.17754.38840.00690.66991.3047-0.3780.8675-1.12450.4903-0.33451.35280.28390.62020.6150.426-0.08411.464111.703115.800937.8526
131.64190.6366-0.60078.97121.39546.61390.0638-0.58390.57790.49960.3893-1.2835-0.10750.081-0.43480.39230.19680.00190.62440.08530.675614.344925.359637.9538
143.1269-0.2321-0.06685.9168-4.73058.5570.2396-0.24410.08670.04730.39791.83970.75180.0676-0.73970.56880.10390.0560.4039-0.11931.038525.719118.53684.0381
151.25930.62010.97063.0349-0.65674.41690.58560.15930.10392.58480.10352.67740.6567-0.8755-0.01081.5433-0.24260.86220.3479-0.04651.410725.706519.85612.8458
169.4701-2.15034.00889.84021.72732.43640.59921.0692-0.632-0.5239-0.17263.0671-4.14620.7224-0.96151.4081-0.13470.00350.64350.15411.085926.551839.0525-3.9118
171.06980.13251.5557.36552.91355.5090.05290.15330.29561.436-0.03850.9876-0.53490.4690.12191.0108-0.08690.43740.5214-0.05540.760934.144135.430312.3017
184.0383-0.881-1.6789.11810.40070.69461.1732-1.3249-0.08781.91510.3922-0.3519-1.0837-2.0173-1.78121.8149-0.16210.53751.33330.0770.601535.295536.942220.0688
192.2428-1.53660.30844.0841-1.98032.1148-0.75360.3479-1.4791-1.24641.00430.0935-0.1413-0.2878-0.26791.6901-0.02491.65830.79980.20831.071418.403141.315421.328
204.4545-0.31412.19962.17572.40034.19-1.02950.4362-0.4477-1.08851.4068-0.7315-1.8195-0.4968-0.64861.48280.03130.60210.69880.18941.103321.957828.035420.7626
212.40150.5444-0.87310.894-1.08283.0199-0.46620.4642-0.45290.4124-0.3535-0.02580.4066-0.23270.76420.8093-0.07360.12210.5981-0.13770.562135.743728.247613.3986
227.79841.9665-0.53035.10492.17124.2046-0.2181-0.1199-0.66920.51760.1522-1.38750.15710.26330.24050.626-0.0434-0.19870.64520.11490.911957.578648.6587.1586
234.9161.1082-0.59127.7489-1.64347.3243-0.43380.8318-0.62970.1454-0.8269-2.10490.93010.15420.54280.70.01790.27520.51530.31480.95751.054936.91382.4148
246.45980.34170.88172.29411.60591.747-0.5758-0.6441-0.83930.3545-0.3361-0.2335-0.52910.53310.42891.5343-0.0022-0.44050.74160.17790.775653.221528.70920.6743
252.7451.102-1.45553.65764.03327.5055-0.38830.334-0.25571.0057-0.4574-0.99890.03330.09760.38271.0316-0.2355-0.47180.6850.38790.648547.61139.149113.4799
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 353 through 449 )
2X-RAY DIFFRACTION2chain 'A' and (resid 450 through 500 )
3X-RAY DIFFRACTION3chain 'A' and (resid 501 through 539 )
4X-RAY DIFFRACTION4chain 'B' and (resid 353 through 389 )
5X-RAY DIFFRACTION5chain 'B' and (resid 390 through 412 )
6X-RAY DIFFRACTION6chain 'B' and (resid 413 through 424 )
7X-RAY DIFFRACTION7chain 'B' and (resid 425 through 449 )
8X-RAY DIFFRACTION8chain 'B' and (resid 450 through 466 )
9X-RAY DIFFRACTION9chain 'B' and (resid 467 through 478 )
10X-RAY DIFFRACTION10chain 'B' and (resid 479 through 497 )
11X-RAY DIFFRACTION11chain 'B' and (resid 498 through 517 )
12X-RAY DIFFRACTION12chain 'B' and (resid 518 through 529 )
13X-RAY DIFFRACTION13chain 'B' and (resid 530 through 539 )
14X-RAY DIFFRACTION14chain 'C' and (resid 353 through 389 )
15X-RAY DIFFRACTION15chain 'C' and (resid 390 through 412 )
16X-RAY DIFFRACTION16chain 'C' and (resid 413 through 424 )
17X-RAY DIFFRACTION17chain 'C' and (resid 425 through 478 )
18X-RAY DIFFRACTION18chain 'C' and (resid 479 through 487 )
19X-RAY DIFFRACTION19chain 'C' and (resid 488 through 499 )
20X-RAY DIFFRACTION20chain 'C' and (resid 500 through 516 )
21X-RAY DIFFRACTION21chain 'C' and (resid 517 through 539 )
22X-RAY DIFFRACTION22chain 'D' and (resid 353 through 412 )
23X-RAY DIFFRACTION23chain 'D' and (resid 413 through 455 )
24X-RAY DIFFRACTION24chain 'D' and (resid 456 through 516 )
25X-RAY DIFFRACTION25chain 'D' and (resid 517 through 539 )

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