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- PDB-4a2m: Structure of the periplasmic domain of the heparin and heparan su... -

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Basic information

Entry
Database: PDB / ID: 4a2m
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/RESPONSE
KeywordsTRANSCRIPTION / BETA-PROPELLER
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 / 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
Biological speciesBACTEROIDES THETAIOTAOMICRON (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 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 1.2Dec 3, 2014Group: Data collection
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
B: TWO-COMPONENT SYSTEM SENSOR HISTIDINE KINASE/RESPONSE
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)363,9398
Polymers362,1014
Non-polymers1,8384
Water00
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)181,9694
Polymers181,0512
Non-polymers9192
Water0
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)181,9694
Polymers181,0512
Non-polymers9192
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)111.120, 80.830, 228.940
Angle α, β, γ (deg.)90.00, 93.96, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22B
32C
42D
13A
23B
33C
43D
14A
24B
34C
44D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A28 - 341
2114B28 - 341
3114C28 - 341
4114D28 - 341
1124A342 - 661
2124B342 - 661
3124C342 - 661
4124D342 - 661
1134A662 - 999
2134B662 - 999
3134C662 - 999
4134D662 - 999
1144A1784 - 1785
2144B1784 - 1785
3144C1784 - 1785
4144D1784 - 1785

NCS ensembles :
ID
1
2
3
4

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.890706, -0.159282, 0.42576), (-0.179925, -0.736583, -0.651976), (0.417456, -0.657324, 0.62742)25.73926, 37.07381, 7.82694
3given(0.880356, -0.043399, -0.472324), (-0.031465, -0.998955, 0.03314), (-0.473269, -0.014313, -0.880802)11.687, 10.91262, 124.35867
4given(-0.980081, 0.198381, -0.009302), (0.146083, 0.751857, 0.642939), (0.134541, 0.628774, -0.765861)70.60918, -52.78065, 80.97154

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Components

#1: Protein
TWO-COMPONENT SYSTEM SENSOR HISTIDINE KINASE/RESPONSE / BT_4663


Mass: 90525.250 Da / Num. of mol.: 4 / 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
#2: Polysaccharide
4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-4)-2-acetamido-2-deoxy-6-O-sulfo-beta-D-glucopyranose


Type: oligosaccharide / Mass: 459.380 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O_6*OSO/3=O/3=O][a21eEA-1a_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc6SO3]{[(4+1)][b-D-4-deoxy-GlcpA]{}}LINUCSPDB-CARE

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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: 2.9 Å3/Da / Density % sol: 60 % / Description: NONE
Crystal growDetails: 0.1 M BIS TRIS PROPANE PH 7.5, 25% PEG 1500.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9798
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 3.4→65.97 Å / Num. obs: 55102 / % possible obs: 97.9 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Biso Wilson estimate: 53.985 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 6.5
Reflection shellResolution: 3.4→3.58 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.6 / % possible all: 95.8

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: APO FORM SEE PAPER

Resolution: 3.4→55.73 Å / Cor.coef. Fo:Fc: 0.85 / Cor.coef. Fo:Fc free: 0.819 / SU B: 118.275 / SU ML: 0.817 / Cross valid method: THROUGHOUT / ESU R Free: 0.665 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED WERE REMOVED
RfactorNum. reflection% reflectionSelection details
Rfree0.28606 2544 4.6 %RANDOM
Rwork0.26784 ---
obs0.26875 52483 97.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 131.71 Å2
Baniso -1Baniso -2Baniso -3
1--1.44 Å20 Å20.05 Å2
2--1.37 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 3.4→55.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23250 0 120 0 23370
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0223914
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.7721.93832606
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.68252967
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.11424.721159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.739153638
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.17215108
X-RAY DIFFRACTIONr_chiral_restr0.0480.23642
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.02118540
X-RAY DIFFRACTIONr_gen_planes_other
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

Refine-ID: X-RAY DIFFRACTION / Type: medium positional / Weight position: 0.5

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A23560.2
12B23560.2
13C23560.18
14D23560.18
21A23420.19
22B23420.22
23C23420.17
24D23420.16
31A9660.21
32B9660.23
33C9660.2
34D9660.2
41A300.35
42B300.37
43C300.38
44D300.62
LS refinement shellResolution: 3.4→3.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.358 3791 -
Rfree-0 -
obs--94.8 %
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)
11.6874-0.8862-0.25332.00570.38691.6565-0.3905-0.1090.08071.38610.14960.3067-0.34860.06860.24091.26650.0383-0.00660.69870.00070.917128.134220.71625.6882
21.5799-1.27330.72672.7489-0.08820.8326-0.3603-0.2827-0.49071.28750.25691.3365-0.0286-0.12760.10340.73140.05650.4860.67160.11871.49749.1834-0.142822.8343
31.24720.29720.88760.53820.09791.39040.22170.0473-0.10590.045-0.0303-0.1380.34870.2305-0.19142.50180.16110.21610.8664-0.04520.898260.3307-9.225678.8105
40.6903-0.11080.20550.64140.00471.35370.08560.11050.09990.1827-0.04470.06380.1512-0.0983-0.04092.292-0.00330.2540.8462-0.01670.815945.639612.353889.6478
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A28 - 783
2X-RAY DIFFRACTION2B28 - 783
3X-RAY DIFFRACTION3C28 - 783
4X-RAY DIFFRACTION4D28 - 783

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