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- PDB-3v9f: Crystal Structure of the extracellular domain of the putative hyb... -

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Basic information

Entry
Database: PDB / ID: 3v9f
TitleCrystal Structure of the extracellular domain of the putative hybrid two component system BT3049 from B. thetaiotaomicron
ComponentsTwo-component system sensor histidine kinase/response regulator, hybrid (One-component system)Two-component regulatory system
KeywordsTRANSCRIPTION / beta-propeller / beta-sandwich
Function / homology
Function and homology information


histidine phosphotransfer kinase activity / protein histidine kinase activity / phosphorelay sensor kinase activity / plasma membrane => GO:0005886 / sequence-specific DNA binding / protein autophosphorylation / DNA-binding transcription factor activity / identical protein binding
Similarity search - Function
Two component regulator propeller / Two component regulator three Y / Two component regulator propeller / Y_Y_Y domain / HTH domain AraC-type, conserved site / Bacterial regulatory proteins, araC family signature. / DNA binding HTH domain, AraC-type / Helix-turn-helix domain / Bacterial regulatory proteins, araC family DNA-binding domain profile. / helix_turn_helix, arabinose operon control protein ...Two component regulator propeller / Two component regulator three Y / Two component regulator propeller / Y_Y_Y domain / HTH domain AraC-type, conserved site / Bacterial regulatory proteins, araC family signature. / DNA binding HTH domain, AraC-type / Helix-turn-helix domain / Bacterial regulatory proteins, araC family DNA-binding domain profile. / helix_turn_helix, arabinose operon control protein / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / YVTN repeat-like/Quinoprotein amine dehydrogenase / CheY-like superfamily / 7 Propeller / Methylamine Dehydrogenase; Chain H / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Homeobox-like domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Two-component system sensor histidine kinase/response regulator, hybrid (One-component system)
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.3 Å
AuthorsZhang, Z. / Liu, Q. / Hendrickson, W.A.
CitationJournal: Febs J. / Year: 2014
Title: Crystal structures of apparent saccharide sensors from histidine kinase receptors prevalent in a human gut symbiont.
Authors: Zhang, Z. / Liu, Q. / Hendrickson, W.A.
History
DepositionDec 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2014Group: Database references
Revision 1.2Oct 8, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Two-component system sensor histidine kinase/response regulator, hybrid (One-component system)
B: Two-component system sensor histidine kinase/response regulator, hybrid (One-component system)
C: Two-component system sensor histidine kinase/response regulator, hybrid (One-component system)
D: Two-component system sensor histidine kinase/response regulator, hybrid (One-component system)


Theoretical massNumber of molelcules
Total (without water)355,0844
Polymers355,0844
Non-polymers00
Water0
1
A: Two-component system sensor histidine kinase/response regulator, hybrid (One-component system)


Theoretical massNumber of molelcules
Total (without water)88,7711
Polymers88,7711
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Two-component system sensor histidine kinase/response regulator, hybrid (One-component system)


Theoretical massNumber of molelcules
Total (without water)88,7711
Polymers88,7711
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Two-component system sensor histidine kinase/response regulator, hybrid (One-component system)


Theoretical massNumber of molelcules
Total (without water)88,7711
Polymers88,7711
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Two-component system sensor histidine kinase/response regulator, hybrid (One-component system)


Theoretical massNumber of molelcules
Total (without water)88,7711
Polymers88,7711
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.927, 114.117, 487.470
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A21 - 793
2010B21 - 793
1020A21 - 793
2020C21 - 793
1030A21 - 793
2030D21 - 793
1040B21 - 793
2040C21 - 793
1050B21 - 793
2050D21 - 793
1060C21 - 793
2060D21 - 793

NCS ensembles :
ID
1
2
3
4
5
6
DetailsThere are 4 biological units in the asymmetric unit.

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Components

#1: Antibody
Two-component system sensor histidine kinase/response regulator, hybrid (One-component system) / Two-component regulatory system


Mass: 88770.977 Da / Num. of mol.: 4 / Fragment: UNP residues 19-798
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: BT_3049 / Plasmid: pSMT3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8A3A5

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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: 3.13 Å3/Da / Density % sol: 60.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 5% PEGMME 2K, 0.1 M Tris buffer pH7.0, vapor diffusion, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
Radiation
IDProtocolScattering typeWavelength-ID
1SINGLE WAVELENGTHx-ray1
2x-ray1
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.3→100 Å / Num. obs: 68485

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
SHELXphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 3.3→39.83 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.867 / WRfactor Rfree: 0.2578 / WRfactor Rwork: 0.2058 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8115 / SU B: 66.065 / SU ML: 0.481 / SU R Cruickshank DPI: 0.5394 / SU Rfree: 0.561 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.561 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2767 3458 5.1 %RANDOM
Rwork0.2251 ---
obs0.2277 68230 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 262.02 Å2 / Biso mean: 82.6607 Å2 / Biso min: 37.16 Å2
Baniso -1Baniso -2Baniso -3
1-3.53 Å20 Å20 Å2
2---2.7 Å20 Å2
3----0.83 Å2
Refinement stepCycle: LAST / Resolution: 3.3→39.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23560 0 0 0 23560
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224124
X-RAY DIFFRACTIONr_angle_refined_deg1.611.92832728
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.92652920
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.83124.9671216
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.098153904
X-RAY DIFFRACTIONr_dihedral_angle_4_deg201592
X-RAY DIFFRACTIONr_chiral_restr0.1210.23536
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02118548
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRms dev position (Å)Weight position
11A1048X-RAY DIFFRACTION0.040.05
12B1048X-RAY DIFFRACTION0.040.05
21A1047X-RAY DIFFRACTION0.040.05
22C1047X-RAY DIFFRACTION0.040.05
31A1053X-RAY DIFFRACTION0.050.05
32D1053X-RAY DIFFRACTION0.050.05
41B1048X-RAY DIFFRACTION0.040.05
42C1048X-RAY DIFFRACTION0.040.05
51B1059X-RAY DIFFRACTION0.060.05
52D1059X-RAY DIFFRACTION0.060.05
61C1054X-RAY DIFFRACTION0.060.05
62D1054X-RAY DIFFRACTION0.060.05
LS refinement shellResolution: 3.3→3.386 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 229 -
Rwork0.312 4287 -
all-4516 -
obs--97.9 %
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)
14.0464-1.6858-0.16315.78220.05483.8697-0.2501-0.60570.21860.18350.3537-0.64120.28140.4976-0.10360.26970.13850.05410.3151-0.21690.337953.8476151.163826.227
23.80111.70920.82784.19140.54134.18060.058-0.4637-0.18770.4138-0.2124-0.45140.14830.2950.15440.07340.11420.00960.68040.11620.335658.2769125.095112.3249
36.24770.898-2.46363.87590.50964.36730.2401-0.78911.39490.10220.00560.6719-0.507-0.0583-0.24570.39590.2236-0.43610.4903-0.65611.26192.158184.217829.7236
45.2561-2.7156-0.37695.5060.01372.99190.57550.59740.5035-0.8395-0.34160.1689-0.118-0.5145-0.23390.2850.0999-0.01330.62860.17330.25496.5839138.456182.7071
54.0279-2.8161-0.24849.07320.34265.8176-0.4208-0.6236-0.35860.99340.72920.21360.1384-0.201-0.30840.43610.1121-0.00140.1667-0.05870.391330.6596199.30640.5241
63.6-0.19442.50634.4371-0.96188.2452-0.5326-0.33550.68190.0431-0.269-0.0749-1.7693-0.14030.80160.81170.0568-0.21040.4462-0.17890.349634.3716153.049771.4983
72.7664-0.7479-1.10535.446-0.29188.099-0.2306-0.0236-0.12020.12910.0868-0.05220.69590.13830.14380.38550.1635-0.11570.1153-0.13770.207123.1724132.104928.0298
85.676-1.37090.78497.592-0.32136.0385-0.6355-1.33580.73661.12040.4328-0.6027-0.8961-0.57040.20270.48280.2569-0.13960.7871-0.02450.284529.9148124.0715130.7889
95.6766-0.25291.89166.51980.70179.3925-0.21370.3106-0.0447-0.59630.330.7675-0.04390.2696-0.11630.5348-0.00820.09990.1147-0.09670.641539.0852171.66381.9557
1051.16041.26658.74720.49016.52510.0407-0.3325-0.23680.27410.2013-0.31550.6016-0.2832-0.24190.41360.15690.0930.7357-0.03060.322544.2162107.789585.6306
115.73770.4516-3.41219.6682-0.16459.55670.0328-0.19161.0131-0.44310.5858-0.5254-0.34360.2251-0.61860.44380.0466-0.37340.1868-0.22940.942718.1326172.02131.3564
124.5697-3.5279-0.95229.3022.48328.4990.07080.1557-0.149-0.4753-0.3902-0.30910.27720.10910.31940.4044-0.061-0.08230.47320.11610.281122.9932107.526586.3802
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 359
2X-RAY DIFFRACTION2B21 - 359
3X-RAY DIFFRACTION3C21 - 359
4X-RAY DIFFRACTION4D21 - 359
5X-RAY DIFFRACTION5A360 - 673
6X-RAY DIFFRACTION6B360 - 673
7X-RAY DIFFRACTION7C360 - 673
8X-RAY DIFFRACTION8D360 - 673
9X-RAY DIFFRACTION9A674 - 793
10X-RAY DIFFRACTION10B674 - 793
11X-RAY DIFFRACTION11C674 - 793
12X-RAY DIFFRACTION12D674 - 793

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