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- PDB-3va6: Crystal Structure of the extracellular domain of the putative hyb... -

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Basic information

Entry
Database: PDB / ID: 3va6
TitleCrystal Structure of the extracellular domain of the putative hybrid two component system BT4673 from B. thetaiotaomicron
ComponentsTwo-component system sensor histidine kinase
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 / identical protein binding / membrane
Similarity search - Function
Two component regulator propeller / Two component regulator three Y / Two component regulator propeller / Y_Y_Y domain / Helix-turn-helix domain / DNA binding HTH domain, AraC-type / 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 / Helix-turn-helix domain / DNA binding HTH domain, AraC-type / 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-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / 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
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsZhang, Z. / Liu, Q. / Hendrickson, W.A.
CitationJournal: To be Published
Title: The Extraellular Domain Structures of Two Potential Saccharide-sensing Two-component Systems from a Human Gut Symbiont
Authors: Zhang, Z. / Liu, Q. / Hendrickson, W.A.
History
DepositionDec 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)174,5982
Polymers174,5982
Non-polymers00
Water1,69394
1
A: Two-component system sensor histidine kinase


Theoretical massNumber of molelcules
Total (without water)87,2991
Polymers87,2991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Two-component system sensor histidine kinase


Theoretical massNumber of molelcules
Total (without water)87,2991
Polymers87,2991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint2 kcal/mol
Surface area64440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.883, 87.883, 430.060
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: TYR / Beg label comp-ID: TYR / End auth comp-ID: TRP / End label comp-ID: TRP / Refine code: _ / Auth seq-ID: 36 - 777 / Label seq-ID: 9 - 750

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsThere are 2 biological units in the asymmetric unit.

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Components

#1: Protein Two-component system sensor histidine kinase


Mass: 87298.969 Da / Num. of mol.: 2 / Fragment: UNP residues 30-777
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.38 Å3/Da / Density % sol: 48.28 %
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 X4A10.97908
2
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 21, 2009
Radiation
IDProtocolScattering typeWavelength-ID
1SINGLE WAVELENGTHx-ray1
2x-ray1
Radiation wavelengthWavelength: 0.97908 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 39798 / % possible obs: 92.2 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 7.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.8-2.854.30.4421,294.4
2.85-2.94.40.41,293.9
2.9-2.964.50.3561,294.3
2.96-3.024.60.3111,293.8
3.02-3.084.70.271,294
3.08-3.154.90.2411,293.9
3.15-3.235.10.2161,293.7
3.23-3.325.30.1951,293.4
3.32-3.425.60.1651,293.4
3.42-3.535.90.1411,293.2
3.53-3.656.30.1311,292.8
3.65-3.86.50.121,292.4
3.8-3.976.90.1151,292.7
3.97-4.187.30.1011,292
4.18-4.447.60.0891,291.6
4.44-4.7980.0791,291.3
4.79-5.278.30.0791,290.6
5.27-6.038.60.0881,290
6.03-7.598.50.0791,288.7
7.59-5080.051,285.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.8 Å46.95 Å
Translation2.8 Å46.95 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.3.0phasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.1data extraction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OTT

3ott


Resolution: 2.8→45.86 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.848 / Occupancy max: 1 / Occupancy min: 0 / SU B: 35.487 / SU ML: 0.341 / Cross valid method: THROUGHOUT / ESU R: 2.067 / ESU R Free: 0.455 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27395 2024 5.1 %RANDOM
Rwork0.21648 ---
obs0.21945 37754 92.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.594 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å20 Å20 Å2
2---0.21 Å20 Å2
3---0.43 Å2
Refinement stepCycle: LAST / Resolution: 2.8→45.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12109 0 0 94 12203
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0212416
X-RAY DIFFRACTIONr_bond_other_d0.0040.028247
X-RAY DIFFRACTIONr_angle_refined_deg1.4821.9316871
X-RAY DIFFRACTIONr_angle_other_deg1.163319988
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.59751485
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.96724.444666
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.598152016
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3731570
X-RAY DIFFRACTIONr_chiral_restr0.0850.21787
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214023
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022687
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRms dev position (Å)Weight position
11A27058X-RAY DIFFRACTION0.110.05
12B27058X-RAY DIFFRACTION0.110.05
LS refinement shellResolution: 2.797→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 131 -
Rwork0.331 2459 -
obs--90.62 %
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)
11.4839-0.7416-0.57970.8844-0.03421.59240.0057-0.204-0.00450.02890.0465-0.0476-0.01080.1272-0.05210.6174-0.0242-0.01140.6915-0.03550.0137-5.43237.5350.383
24.5269-0.7833-1.61834.5280.50895.2213-0.34680.173-0.52590.3105-0.11610.47030.5183-0.22360.46290.75120.0130.17640.729-0.06130.2611-30.37111.76-34.928
34.529-0.6543-1.37353.41950.95342.9157-0.0048-0.0146-0.233-0.181-0.1134-0.2290.08640.10670.11810.72290.0187-0.01160.6680.06030.042215.00615.219-18.339
40.8527-0.06070.36531.23180.15961.91-0.0427-0.064-0.007-0.01330.01360.1013-0.0965-0.15990.02910.6144-0.01740.0220.6716-0.00040.0132-41.65345.643-24.913
52.05830.52840.43434.02350.18211.4657-0.07210.04340.2281-0.0865-0.05170.2706-0.0038-0.16920.12380.6491-0.00520.00090.72170.0210.0426.9655.945-29.599
62.5737-0.3594-0.98233.63450.26747.58050.09730.10.0573-0.1162-0.1031-0.1164-0.00930.32670.00580.68770.00480.04090.66530.0230.0088-29.22249.453-57.798
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A36 - 334
2X-RAY DIFFRACTION2A336 - 659
3X-RAY DIFFRACTION3A660 - 785
4X-RAY DIFFRACTION4B36 - 335
5X-RAY DIFFRACTION5B336 - 659
6X-RAY DIFFRACTION6B660 - 778

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