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- PDB-4a2l: Structure of the periplasmic domain of the heparin and heparan su... -

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Basic information

Entry
Database: PDB / ID: 4a2l
TitleStructure of the periplasmic domain of the heparin and heparan sulphate sensing hybrid two component system BT4663 in apo and ligand bound forms
ComponentsTWO-COMPONENT SYSTEM SENSOR HISTIDINE KINASE/RESPONSETwo-component regulatory system
KeywordsTRANSCRIPTION / BETA-PROPELLER
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 / Protein of unknown function DUF5074 / Domain of unknown function (DUF5074) / 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 / Protein of unknown function DUF5074 / Domain of unknown function (DUF5074) / 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
OXALOACETATE ION / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / histidine kinase
Similarity search - Component
Biological speciesBACTEROIDES THETAIOTAOMICRON (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsLowe, E.C. / Basle, A. / Czjzek, M. / Firbank, S.J. / Bolam, D.N.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: A Scissor Blade-Like Closing Mechanism Implicated in Transmembrane Signaling in a Bacteroides Hybrid Two-Component System.
Authors: Lowe, E.C. / Basle, A. / Czjzek, M. / Firbank, S.J. / Bolam, D.N.
History
DepositionSep 27, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1May 23, 2012Group: Other
Revision 1.2Nov 19, 2014Group: Data collection

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TWO-COMPONENT SYSTEM SENSOR HISTIDINE KINASE/RESPONSE
B: TWO-COMPONENT SYSTEM SENSOR HISTIDINE KINASE/RESPONSE
C: TWO-COMPONENT SYSTEM SENSOR HISTIDINE KINASE/RESPONSE
D: TWO-COMPONENT SYSTEM SENSOR HISTIDINE KINASE/RESPONSE
E: TWO-COMPONENT SYSTEM SENSOR HISTIDINE KINASE/RESPONSE
F: TWO-COMPONENT SYSTEM SENSOR HISTIDINE KINASE/RESPONSE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)546,96835
Polymers543,1526
Non-polymers3,81629
Water5,423301
1
A: TWO-COMPONENT SYSTEM SENSOR HISTIDINE KINASE/RESPONSE
B: TWO-COMPONENT SYSTEM SENSOR HISTIDINE KINASE/RESPONSE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,28912
Polymers181,0512
Non-polymers1,23810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: TWO-COMPONENT SYSTEM SENSOR HISTIDINE KINASE/RESPONSE
D: TWO-COMPONENT SYSTEM SENSOR HISTIDINE KINASE/RESPONSE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,78915
Polymers181,0512
Non-polymers1,73913
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
E: TWO-COMPONENT SYSTEM SENSOR HISTIDINE KINASE/RESPONSE
F: TWO-COMPONENT SYSTEM SENSOR HISTIDINE KINASE/RESPONSE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,8898
Polymers181,0512
Non-polymers8396
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)342.468, 342.468, 97.852
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A28 - 327
2114B28 - 327
3114C28 - 327
4114D28 - 327
5114E28 - 327
6114F28 - 327
1214A375 - 635
2214B375 - 635
3214C375 - 635
4214D375 - 635
5214E375 - 635
6214F375 - 635
1314A687 - 784
2314B687 - 784
3314C687 - 784
4314D687 - 784
5314E687 - 784
6314F687 - 784

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.647943, -0.021079, 0.761397), (-0.009868, -0.999301, -0.036062), (0.761625, -0.03088, 0.647282)76.18772, 86.26371, -34.20935
3given(0.407483, -0.913192, -0.006189), (-0.913118, -0.407529, 0.011618), (-0.013132, 0.000917, -0.999913)21.78255, 193.91292, 41.45382
4given(-0.24148, 0.603253, -0.760114), (0.912216, 0.408278, 0.034223), (0.330983, -0.685124, -0.648888)87.52747, -109.76499, 3.34558
5given(0.636864, -0.090238, 0.765677), (0.171406, 0.984844, -0.026502), (-0.751681, 0.148119, 0.642679)-55.21972, -37.89225, 54.60938
6given(-0.986301, 0.164835, -0.006325), (-0.164722, -0.986218, -0.015522), (-0.008796, -0.014267, 0.99986)153.60167, 124.57809, -38.01571

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
TWO-COMPONENT SYSTEM SENSOR HISTIDINE KINASE/RESPONSE / Two-component regulatory system / BT_4663


Mass: 90525.250 Da / Num. of mol.: 6 / Fragment: PERIPLASMIC DOMAIN, RESIDUES 1-787
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACTEROIDES THETAIOTAOMICRON (bacteria)
Strain: VPI-5482 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q89YR8

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Non-polymers , 8 types, 330 molecules

#2: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#7: Chemical ChemComp-OAA / OXALOACETATE ION / Oxaloacetic acid


Mass: 131.064 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H3O5
#8: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL / Polyethylene glycol


Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 301 / 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: 3.1 Å3/Da / Density % sol: 60 % / Description: NONE
Crystal growDetails: 0.1 M MMT BUFFER PH 8.0, 25 % PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9796
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.6→71.12 Å / Num. obs: 190851 / % possible obs: 95.1 % / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Biso Wilson estimate: 59.026 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.5
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 3.7 / % possible all: 75.7

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
iMOSFLMdata reduction
SCALAdata scaling
SHELXCDEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.6→296.59 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.918 / SU B: 19.836 / SU ML: 0.197 / Cross valid method: THROUGHOUT / ESU R: 0.487 / ESU R Free: 0.277 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED ATOMS WERE REMOVED.
RfactorNum. reflection% reflectionSelection details
Rfree0.23124 9606 5 %RANDOM
Rwork0.18557 ---
obs0.18787 181114 94.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.76 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å20.41 Å20 Å2
2--0.82 Å20 Å2
3----1.23 Å2
Refinement stepCycle: LAST / Resolution: 2.6→296.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms35314 0 224 301 35839
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0236336
X-RAY DIFFRACTIONr_bond_other_d0.0010.0224004
X-RAY DIFFRACTIONr_angle_refined_deg1.3921.93849348
X-RAY DIFFRACTIONr_angle_other_deg0.892358407
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5254460
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.49124.6511774
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.553155750
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.65315177
X-RAY DIFFRACTIONr_chiral_restr0.1090.25431
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0240867
X-RAY DIFFRACTIONr_gen_planes_other0.0010.027654
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_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 8154 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.50.5
2Bmedium positional0.510.5
3Cmedium positional0.50.5
4Dmedium positional0.50.5
5Emedium positional0.480.5
6Fmedium positional0.540.5
1Amedium thermal3.662
2Bmedium thermal3.342
3Cmedium thermal3.192
4Dmedium thermal3.182
5Emedium thermal2.962
6Fmedium thermal3.862
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 523 -
Rwork0.311 10047 -
obs--72.54 %
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)
10.63030.07780.18540.67370.50981.5585-0.02370.04380.1027-0.132-0.04190.0402-0.171-0.04480.06560.0310.0021-0.01330.06720.03260.030865.562451.765316.0473
21.1486-0.88460.280.9294-0.20410.5268-0.0155-0.0648-0.1248-0.0334-0.00120.05590.1637-0.18360.01670.1029-0.0170.04170.13480.01630.032345.140333.120425.5533
30.9411-0.0580.54030.60280.16461.2150.0389-0.0925-0.0184-0.005-0.09620.070.0368-0.1310.05720.04130.00220.01390.0308-0.00670.024148.22217.888424.0242
42.185-0.8369-0.21140.57020.13830.35170.1060.06190.0894-0.0659-0.0973-0.087-0.13630.025-0.00870.1297-0.0134-0.010.08940.06670.054156.724244.218914.1062
50.8027-0.8697-0.22111.40590.13020.3428-0.0805-0.11420.08670.07150.1047-0.0791-0.02860.1662-0.02420.13930.0165-0.06230.13430.00380.0529121.557171.796665.1851
60.6359-0.0408-0.2740.5339-0.27041.2615-0.0729-0.0026-0.0617-0.0913-0.0281-0.01260.1673-0.00130.1010.0444-0.00920.01110.02390.00720.033798.353756.796155.1994
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A28 - 327
2X-RAY DIFFRACTION1A328 - 374
3X-RAY DIFFRACTION1A375 - 635
4X-RAY DIFFRACTION1A636 - 686
5X-RAY DIFFRACTION1A687 - 784
6X-RAY DIFFRACTION2B28 - 327
7X-RAY DIFFRACTION2B328 - 374
8X-RAY DIFFRACTION2B375 - 635
9X-RAY DIFFRACTION2B636 - 686
10X-RAY DIFFRACTION2B687 - 784
11X-RAY DIFFRACTION3C28 - 327
12X-RAY DIFFRACTION3C328 - 374
13X-RAY DIFFRACTION3C375 - 635
14X-RAY DIFFRACTION3C636 - 686
15X-RAY DIFFRACTION3C687 - 784
16X-RAY DIFFRACTION4D28 - 327
17X-RAY DIFFRACTION4D328 - 374
18X-RAY DIFFRACTION4D375 - 635
19X-RAY DIFFRACTION4D636 - 686
20X-RAY DIFFRACTION4D687 - 784
21X-RAY DIFFRACTION5E28 - 327
22X-RAY DIFFRACTION5E328 - 374
23X-RAY DIFFRACTION5E375 - 635
24X-RAY DIFFRACTION5E636 - 686
25X-RAY DIFFRACTION5E687 - 784
26X-RAY DIFFRACTION6F28 - 327
27X-RAY DIFFRACTION6F328 - 374
28X-RAY DIFFRACTION6F375 - 635
29X-RAY DIFFRACTION6F636 - 686
30X-RAY DIFFRACTION6F687 - 784

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