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- PDB-3zx6: Structure of Hamp(AF1503)-Tsr fusion - Hamp (A291V) mutant -

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Basic information

Entry
Database: PDB / ID: 3zx6
TitleStructure of Hamp(AF1503)-Tsr fusion - Hamp (A291V) mutant
ComponentsHAMP, METHYL-ACCEPTING CHEMOTAXIS PROTEIN I
KeywordsSIGNALING / HAMP DOMAIN / TSR RECEPTOR / FUSION
Function / homology
Function and homology information


regulation of protein histidine kinase activity / detection of chemical stimulus / methyl accepting chemotaxis protein complex / protein trimerization / regulation of bacterial-type flagellum-dependent cell motility / regulation of chemotaxis / signal complex assembly / receptor clustering / histidine kinase / phosphorelay signal transduction system ...regulation of protein histidine kinase activity / detection of chemical stimulus / methyl accepting chemotaxis protein complex / protein trimerization / regulation of bacterial-type flagellum-dependent cell motility / regulation of chemotaxis / signal complex assembly / receptor clustering / histidine kinase / phosphorelay signal transduction system / cellular response to amino acid stimulus / cell motility / protein homooligomerization / chemotaxis / kinase activity / transmembrane signaling receptor activity / signal transduction / metal ion binding / identical protein binding / plasma membrane
Similarity search - Function
Methyl-accepting chemotaxis protein / Methyl-accepting chemotaxis protein, four helix bundle domain superfamily / Homologues of the ligand binding domain of Tar / Chemotaxis methyl-accepting receptor, methyl-accepting site / Bacterial chemotaxis sensory transducers signature. / : / Chemotaxis methyl-accepting receptor Tar-related, ligand-binding / Tar ligand binding domain homologue / : / Chemotaxis methyl-accepting receptor ...Methyl-accepting chemotaxis protein / Methyl-accepting chemotaxis protein, four helix bundle domain superfamily / Homologues of the ligand binding domain of Tar / Chemotaxis methyl-accepting receptor, methyl-accepting site / Bacterial chemotaxis sensory transducers signature. / : / Chemotaxis methyl-accepting receptor Tar-related, ligand-binding / Tar ligand binding domain homologue / : / Chemotaxis methyl-accepting receptor / Methyl-accepting chemotaxis protein (MCP) signalling domain / Methyl-accepting chemotaxis protein (MCP) signalling domain / Bacterial chemotaxis sensory transducers domain profile. / Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer). / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
histidine kinase / Methyl-accepting chemotaxis protein I
Similarity search - Component
Biological speciesARCHAEOGLOBUS FULGIDUS (archaea)
ESCHERICHIA COLI K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsZeth, K. / Ferris, H.U. / Lupas, A.L.
CitationJournal: J.Struct.Biol. / Year: 2014
Title: Axial Helix Rotation as a Mechanism for Signal Regulation Inferred from the Crystallographic Analysis of the E. Coli Serine Chemoreceptor.
Authors: Ferris, H.U. / Zeth, K. / Hulko, M. / Dunin-Horkawicz, S. / Lupas, A.N.
History
DepositionAug 8, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2014Group: Data collection / Database references
Revision 1.2Jun 11, 2014Group: Database references
Revision 1.3Mar 15, 2017Group: Source and taxonomy
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: HAMP, METHYL-ACCEPTING CHEMOTAXIS PROTEIN I
B: HAMP, METHYL-ACCEPTING CHEMOTAXIS PROTEIN I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,3434
Polymers72,2722
Non-polymers712
Water1,36976
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11610 Å2
ΔGint-134.8 kcal/mol
Surface area30490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.220, 80.020, 139.170
Angle α, β, γ (deg.)90.00, 110.78, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein HAMP, METHYL-ACCEPTING CHEMOTAXIS PROTEIN I / MCP-I / SERINE CHEMORECEPTOR PROTEIN / TSR


Mass: 36136.066 Da / Num. of mol.: 2
Fragment: HAMP RESIDUES 278-326, METHYL-ACCEPTING CHEMOTAXIS PROTEIN I RESIDUES 264-551
Mutation: YES
Source method: isolated from a genetically manipulated source
Details: CHIMERA, THREE RESIDUE LINKER INTERNALLY IN METHYL-ACCEPTING CHEMOTAXIS PROTEIN DOMAIN
Source: (gene. exp.) ARCHAEOGLOBUS FULGIDUS (archaea), (gene. exp.) ESCHERICHIA COLI K-12 (bacteria)
Strain: DSM 4304 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O28769, UniProt: P02942
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ALA 291 TO VAL ENGINEERED RESIDUE IN CHAIN B, ALA 291 TO VAL
Sequence detailsTHREE RESIDUE QQQ LINKER INSERTED IN UNP P02942.

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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: 4.04 Å3/Da / Density % sol: 69.57 % / Description: NONE
Crystal growpH: 7 / Details: PH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: MARRESEARCH MX-225 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→40 Å / Num. obs: 32412 / % possible obs: 96.1 % / Observed criterion σ(I): 2 / Redundancy: 2.6 % / Biso Wilson estimate: 60 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.57
Reflection shellResolution: 2.65→2.75 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2 / % possible all: 96.2

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZRX

3zrx


Resolution: 2.65→29.48 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.922 / SU B: 27.79 / SU ML: 0.245 / Cross valid method: THROUGHOUT / ESU R: 0.387 / ESU R Free: 0.298 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.28263 1553 5 %RANDOM
Rwork0.22874 ---
obs0.2314 29577 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.377 Å2
Baniso -1Baniso -2Baniso -3
1--3.52 Å20 Å2-6.39 Å2
2--3.44 Å20 Å2
3----4.47 Å2
Refinement stepCycle: LAST / Resolution: 2.65→29.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4436 0 2 76 4514
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0224456
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.941.9516027
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1395604
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.08225.441204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.93515787
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4911541
X-RAY DIFFRACTIONr_chiral_restr0.130.2744
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023320
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_it0.821.52994
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.67824773
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.1531462
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.864.51254
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
LS refinement shellResolution: 2.65→2.718 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 103 -
Rwork0.329 2020 -
obs--100 %
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)
17.9859-3.31184.6271.8141-3.4568.9807-0.7964-0.10411.71910.25780.076-0.4984-0.4247-0.42250.72040.24570.0488-0.29640.1262-0.16060.7084-103.76511.4174-131.2447
24.21480.75146.2730.16191.10079.5553-0.0260.06240.01830.0417-0.03570.01460.00610.08290.06170.1522-0.0299-0.00150.1448-0.0110.1188-68.04633.5028-82.7311
31.50040.55981.29540.86330.2272.31370.1651-0.091-0.09190.1723-0.1006-0.04290.2777-0.053-0.06450.0975-0.02280.04910.29070.00790.1157-9.486110.913312.1996
42.38480.3663.27830.11320.36795.13250.27090.05160.00220.02720.02730.09130.64770.0392-0.29830.21-0.0472-0.07470.31090.04670.1605-27.66559.2459-16.4492
55.40610.31826.68650.2430.25158.4733-0.01950.04120.29860.0909-0.25580.06380.04680.19590.27530.1741-0.1383-0.05470.40470.00820.0793-72.18225.2905-95.1758
61.88991.51511.81775.2454-0.49233.0714-0.21030.2354-0.0591-0.30160.1170.03580.01210.35870.09330.1196-0.06850.07610.27110.02440.122-94.0833-7.1282-137.1429
72.7350.63684.56750.19041.01738.06930.2217-0.3768-0.02190.0466-0.1426-0.00250.5236-0.6372-0.07910.1279-0.0142-0.00060.15280.00030.1215-52.40025.259-60.0257
84.59441.14844.11481.19590.73597.35290.2312-0.0685-0.14330.1034-0.0029-0.13880.18640.1393-0.22830.08210.01050.07140.2179-0.03210.14532.047513.765815.0712
96.53311.87957.75740.5472.22419.8422-0.155-0.1910.317-0.0706-0.04790.08010.1075-0.3120.20290.3241-0.1658-0.11360.27330.11030.1381-45.6219.6968-47.4534
105.14980.70755.88970.14091.779928.9030.8102-0.1639-0.77280.128-0.0667-0.10590.916-1.0304-0.74340.411-0.329-0.20440.3580.10910.1417-83.8155-8.2252-107.3593
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 29
2X-RAY DIFFRACTION2A30 - 135
3X-RAY DIFFRACTION3A136 - 183
4X-RAY DIFFRACTION4A184 - 255
5X-RAY DIFFRACTION5A256 - 305
6X-RAY DIFFRACTION6B2 - 44
7X-RAY DIFFRACTION7B45 - 157
8X-RAY DIFFRACTION8B158 - 205
9X-RAY DIFFRACTION9B206 - 280
10X-RAY DIFFRACTION10B281 - 304

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