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- PDB-3zrx: The high resolution structure of a dimeric Hamp-Dhp fusion displa... -

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Basic information

Entry
Database: PDB / ID: 3zrx
TitleThe high resolution structure of a dimeric Hamp-Dhp fusion displays strong asymmetry
ComponentsAF1503 PROTEIN, OSMOLARITY SENSOR PROTEIN ENVZ
KeywordsSIGNALING PROTEIN / OSMOREGULATION / OMPR / OMPC
Function / homology
Function and homology information


response to osmotic stress / phosphorelay sensor kinase activity / histidine kinase / phosphorelay signal transduction system / phosphoprotein phosphatase activity / kinase activity / outer membrane-bounded periplasmic space / protein autophosphorylation / signal transduction / protein homodimerization activity ...response to osmotic stress / phosphorelay sensor kinase activity / histidine kinase / phosphorelay signal transduction system / phosphoprotein phosphatase activity / kinase activity / outer membrane-bounded periplasmic space / protein autophosphorylation / signal transduction / protein homodimerization activity / ATP binding / metal ion binding / identical protein binding / plasma membrane / cytosol
Similarity search - Function
: / : / Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain ...: / : / Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain / 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 / Histidine kinase domain / Histidine kinase domain profile. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
histidine kinase / Sensor histidine kinase EnvZ
Similarity search - Component
Biological speciesARCHAEOGLOBUS FULGIDUS (archaea)
ESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.25 Å
AuthorsZeth, K. / Hulko, M. / Martin, J.
CitationJournal: Structure / Year: 2012
Title: Mechanism of Regulation of Receptor Histidine Kinases.
Authors: Ferris, H.U. / Dunin-Horkawicz, S. / Hornig, N. / Hulko, M. / Martin, J. / Schultz, J.E. / Zeth, K. / Lupas, A.N. / Coles, M.
History
DepositionJun 20, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2012Group: Database references / Version format compliance
Revision 1.2Mar 15, 2017Group: Source and taxonomy
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AF1503 PROTEIN, OSMOLARITY SENSOR PROTEIN ENVZ
B: AF1503 PROTEIN, OSMOLARITY SENSOR PROTEIN ENVZ


Theoretical massNumber of molelcules
Total (without water)26,1682
Polymers26,1682
Non-polymers00
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-50.4 kcal/mol
Surface area12340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.110, 57.400, 51.620
Angle α, β, γ (deg.)90.00, 107.32, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein AF1503 PROTEIN, OSMOLARITY SENSOR PROTEIN ENVZ / HAMP-DHP-FUSION PROTEIN


Mass: 13083.843 Da / Num. of mol.: 2 / Fragment: RESIDUES 278-327,229-289
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARCHAEOGLOBUS FULGIDUS (archaea), (gene. exp.) ESCHERICHIA COLI (E. coli)
Strain: DSM 4304, K-12 / Description: PCR FROM E. COLI WT DNA AND A. FULGIDUS WT DNA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O28769, UniProt: P0AEJ4, histidine kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS PROTEIN STRUCTURE COMPRISES RESIDUES OF THE PROTEIN AF1503 FROM A. FULGIDUS AND THE OSMOLARITY ...THIS PROTEIN STRUCTURE COMPRISES RESIDUES OF THE PROTEIN AF1503 FROM A. FULGIDUS AND THE OSMOLARITY SENSING PROTEIN FROM E. COLI

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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: 1.95 Å3/Da / Density % sol: 36.98 % / Description: NONE
Crystal growpH: 4.6
Details: 0.02 M CALCIUM CHLORIDE 0.1 M SODIUM ACETATE 30% MPD, PH4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.068
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.068 Å / Relative weight: 1
ReflectionResolution: 1.25→20 Å / Num. obs: 52510 / % possible obs: 90.7 % / Observed criterion σ(I): 1.25 / Redundancy: 4.3 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 18.3
Reflection shellResolution: 1.25→1.28 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 1.8 / % possible all: 90.1

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
SHARPphasing
DMphasing
BUCCANEERmodel building
RefinementMethod to determine structure: SAD
Starting model: PDB ENTRY 2ASM

2asm


Resolution: 1.25→18.84 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.784 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.19987 2806 5.1 %RANDOM
Rwork0.15054 ---
obs0.15309 52510 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.428 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å2-0.12 Å2
2--0.25 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.25→18.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1752 0 0 217 1969
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0221887
X-RAY DIFFRACTIONr_bond_other_d0.0050.021317
X-RAY DIFFRACTIONr_angle_refined_deg2.1611.9962575
X-RAY DIFFRACTIONr_angle_other_deg1.14333249
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.355257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.98424.46894
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.87115385
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6341521
X-RAY DIFFRACTIONr_chiral_restr0.1380.2310
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022113
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02352
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_it2.6371.51164
X-RAY DIFFRACTIONr_mcbond_other0.9781.5463
X-RAY DIFFRACTIONr_mcangle_it3.84421907
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.1673723
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it9.1574.5649
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.68533204
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.25→1.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 213 -
Rwork0.228 3845 -
obs--99.31 %
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)
10.4019-0.04240.4450.0608-0.08860.5275-0.01580.0037-0.00310.01230.01150.005-0.02760.00030.00430.01-0.00070.00530.02520.00090.039441.4214.51733.033
21.0065-0.04120.20510.359-0.01060.0777-0.0096-0.03230.00730.00160.0033-0.026-0.0018-0.00890.00630.0080.00050.00770.0259-0.00040.034946.4094.61224.281
30.2703-0.07290.28060.0569-0.09440.3018-0.0038-0.00550.01190.0173-0.00440.0126-0.01380.00030.00830.012-0.00140.00730.0275-0.00030.038426.7437.7797.678
40.6715-0.4065-0.23480.64330.07870.118-0.0095-0.01310.066-0.0080.0175-0.060.01340.0035-0.0080.00880.00060.00780.023600.04710.10617.12-3.069
50.7788-0.07490.48850.0533-0.05610.4631-0.0157-0.02040.01620.00270.0066-0.0007-0.0037-0.00920.00910.00910.00050.00730.0224-0.00050.03769.97910.5210.188
60.3566-0.50780.48971.2211-0.6560.9014-0.03540.01910.01740.075-0.0002-0.0758-0.03870.01180.03550.0108-0.00140.00360.0228-0.00240.042548.487-8.68828.285
70.1156-0.05960.0860.1818-0.05070.84680.00340.0033-0.01-0.0068-0.00380.00390.0313-0.01230.00040.0084-0.00090.00410.0235-0.0010.039738.382-10.23822.964
80.3725-0.01880.53290.10210.20071.33480.01490.0101-0.01140.0111-0.01120.01340.0208-0.024-0.00370.0140.00150.00730.024700.038734.713-4.85528.176
90.2547-0.16760.15150.1105-0.09940.21020.0050.00440.0034-0.0046-0.0048-0.00290.00810.0044-0.00020.0102-0.00020.00680.02200.03944.8655.288-1.479
102.5986-0.0632-0.80790.0403-0.00160.29170.0044-0.048-0.06420.0139-0.00030.02530.00780.0179-0.00410.01770.00010.01020.0230.00030.044120.5110.146-3.105
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A278 - 298
2X-RAY DIFFRACTION2A299 - 323
3X-RAY DIFFRACTION3A324 - 345
4X-RAY DIFFRACTION4A346 - 366
5X-RAY DIFFRACTION5A367 - 388
6X-RAY DIFFRACTION6B279 - 292
7X-RAY DIFFRACTION7B293 - 307
8X-RAY DIFFRACTION8B308 - 332
9X-RAY DIFFRACTION9B333 - 376
10X-RAY DIFFRACTION10B377 - 388

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