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- PDB-3ott: Crystal Structure of the extracellular domain of the putative one... -

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Basic information

Entry
Database: PDB / ID: 3ott
TitleCrystal Structure of the extracellular domain of the putative one component system BT4673 from B. thetaiotaomicron
ComponentsTwo-component system sensor histidine kinaseTwo-component regulatory system
KeywordsTRANSCRIPTION / beta-propeller / beta-sandwich
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity / sequence-specific DNA binding / DNA-binding transcription factor activity / membrane / identical protein binding
Similarity search - Function
Two component regulator propeller / Two component regulator three Y / Two component regulator propeller / Y_Y_Y domain / 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 ...Two component regulator propeller / Two component regulator three Y / Two component regulator propeller / Y_Y_Y domain / 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 / Quinoprotein alcohol dehydrogenase-like superfamily / Histidine kinase domain / Histidine kinase domain profile. / YVTN repeat-like/Quinoprotein amine dehydrogenase / 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
HEXATANTALUM DODECABROMIDE / histidine kinase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsZhang, Z. / Liu, Q. / Hendrickson, W.A.
Citation
Journal: 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.
#1: Journal: To be Published
Title: Multi-crystal Anomalous Diffraction for Low Resolution Macromolecular Phasing
History
DepositionSep 13, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2014Group: Database references
Revision 1.2Oct 1, 2014Group: Database references
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
B: Two-component system sensor histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,7234
Polymers174,6342
Non-polymers4,0892
Water5,044280
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5250 Å2
ΔGint-0 kcal/mol
Surface area64080 Å2
MethodPISA
2
A: Two-component system sensor histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,3622
Polymers87,3171
Non-polymers2,0451
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Two-component system sensor histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,3622
Polymers87,3171
Non-polymers2,0451
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.173, 88.173, 432.956
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
DetailsThere are 2 biological units in the asymmetric unit .

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Components

#1: Protein Two-component system sensor histidine kinase / Two-component regulatory system


Mass: 87317.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: BT_4673 / Plasmid: pET22b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q89YQ8
#2: Chemical ChemComp-TBR / HEXATANTALUM DODECABROMIDE / DODECABROMOHEXATANTALUM


Mass: 2044.535 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br12Ta6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 2.41 Å3/Da / Density % sol: 48.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5
Details: 5% PEGMME 2K, 10% tascimate acid pH7.0 plus 0.1 M cacodylate buffer pH5.5, vapor diffusion, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X4A11.25441
2
DetectorDetector: CCD
Radiation
IDProtocolScattering typeWavelength-ID
1SADx-ray1
2x-ray1
Radiation wavelengthWavelength: 1.25441 Å / Relative weight: 1
ReflectionNumber: 1080649 / Rmerge(I) obs: 0.132 / D res high: 2 Å / Num. obs: 194236 / % possible obs: 89.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
8.9489.8237798.310.026
6.328.94439199.410.039
5.166.32567899.710.046
4.475.16682899.910.039
44.47764799.910.045
3.654850710010.061
3.383.65926610010.076
3.163.38995310010.11
2.983.161059210010.151
2.832.981112810010.215
2.72.831179810010.303
2.582.71226110010.414
2.482.581286810010.509
2.392.481332210010.647
2.312.391381310010.8
2.242.311409298.410.95
2.172.241229983.410.972
2.112.171029067.710.95
2.052.11907858.211.217
22.05804850.411.64
ReflectionHighest resolution: 2 Å / Num. obs: 194236 / % possible obs: 89.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 35.168 Å2 / Rmerge(I) obs: 0.132 / Net I/σ(I): 11.9
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2-2.050.0160.6161048048150.4
2.05-2.110.0160.8198949078158.2
2.11-2.170.0161.12431210290167.7
2.17-2.240.0161.54602312299183.4
2.24-2.310.0162.17613814092198.4
2.31-2.390.0162.887427138131100
2.39-2.480.0163.584285133221100
2.48-2.580.0164.381599128681100
2.58-2.70.0165.378087122611100
2.7-2.830.016775243117981100
2.83-2.980.0169.671269111281100
2.98-3.160.01613.167923105921100
3.16-3.380.01617.16391699531100
3.38-3.650.01623.65960992661100
3.65-40.01628.35485185071100
4-4.470.01636.3492367647199.9
4.47-5.160.01640.9441946828199.9
5.16-6.320.01635.2369135678199.7
6.32-8.940.01639.9284734391199.4
8.94-89.80.01660151532377198.3

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→39.27 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.899 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 13.994 / SU ML: 0.166 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2533 3840 5 %RANDOM
Rwork0.1945 ---
obs0.1974 76749 99.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 58.46 Å2 / Biso mean: 33.171 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å20 Å2
2---0.2 Å20 Å2
3---0.39 Å2
Refinement stepCycle: LAST / Resolution: 2.3→39.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11999 0 36 280 12315
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02112362
X-RAY DIFFRACTIONr_angle_refined_deg1.7661.92416821
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.29151468
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.3924.387661
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.68152000
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2361571
X-RAY DIFFRACTIONr_chiral_restr0.130.21773
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0219620
X-RAY DIFFRACTIONr_mcbond_it0.9781.57306
X-RAY DIFFRACTIONr_mcangle_it1.817211815
X-RAY DIFFRACTIONr_scbond_it2.89635056
X-RAY DIFFRACTIONr_scangle_it4.3534.55004
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 288 -
Rwork0.243 5211 -
all-5499 -
obs--98.2 %
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)
10.5555-0.2575-0.33990.5470.06270.5147-0.0159-0.10740.00670.01020.0467-0.02630.00540.0668-0.03080.0786-0.015-0.00050.1719-0.00670.005138.87682216.797
24.7428-1.8193-2.37494.01011.13054.1012-0.49530.4361-0.54510.2309-0.14430.17860.4743-0.17340.63960.1478-0.03710.14580.0854-0.04440.157313.62856.191181.148
31.8446-0.0256-0.52692.57130.05531.59950.02310.0213-0.0589-0.1392-0.1089-0.12380.13750.02060.08580.07590.02550.02280.10050.01150.013257.95659.392198.287
40.44370.10420.08060.47190.09660.7097-0.0167-0.0433-0.0324-0.00250.02710.0194-0.0574-0.0608-0.01050.08150.0020.01430.1229-0.00510.02322.7690.124191.643
51.110.18980.26291.17530.07210.6831-0.04580.11970.0371-0.0601-0.01960.0814-0.0262-0.01170.06540.0681-0.00510.00290.12710.00910.013551.941100.192187
61.75560.2756-0.28052.190.36523.86540.04060.03610.1393-0.0704-0.1106-0.09490.04920.29030.070.09020.01570.01710.09510.01990.021616.02594.331159.789
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A36 - 334
2X-RAY DIFFRACTION2A336 - 651
3X-RAY DIFFRACTION3A655 - 785
4X-RAY DIFFRACTION4B35 - 334
5X-RAY DIFFRACTION5B336 - 652
6X-RAY DIFFRACTION6B653 - 777

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