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

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Basic information

Entry
Database: PDB / ID: 3zrv
TitleThe high resolution structure of a dimeric Hamp-Dhp fusion displays asymmetry - A291F mutant
ComponentsHAMP, OSMOLARITY SENSOR PROTEIN ENVZ
KeywordsSIGNALING PROTEIN / SIGNALLING PROTEIN / HAMP / SIGNALLING
Function / homology
Function and homology information


response to osmotic stress / histidine kinase / phosphorelay signal transduction system / phosphoprotein phosphatase activity / phosphorelay sensor kinase activity / outer membrane-bounded periplasmic space / protein autophosphorylation / phosphorylation / signal transduction / protein homodimerization activity ...response to osmotic stress / histidine kinase / phosphorelay signal transduction system / phosphoprotein phosphatase activity / phosphorelay sensor kinase activity / outer membrane-bounded periplasmic space / protein autophosphorylation / phosphorylation / signal transduction / protein homodimerization activity / ATP binding / identical protein binding / membrane / metal ion 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/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal ...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/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / 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 / Histidine kinase/HSP90-like ATPase superfamily / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HAMP domain-containing protein / Sensor histidine kinase EnvZ
Similarity search - Component
Biological speciesARCHAEOGLOBUS FULGIDUS (archaea)
ESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsZeth, K. / Hulko, M. / Ferris, H.U. / 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 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2012Group: Database references / Version format compliance
Revision 1.2Mar 15, 2017Group: Source and taxonomy
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
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: HAMP, OSMOLARITY SENSOR PROTEIN ENVZ
B: HAMP, OSMOLARITY SENSOR PROTEIN ENVZ


Theoretical massNumber of molelcules
Total (without water)26,3702
Polymers26,3702
Non-polymers00
Water5,170287
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-42.1 kcal/mol
Surface area12770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.260, 56.790, 83.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HAMP, OSMOLARITY SENSOR PROTEIN ENVZ / HAMP-DHP-FUSION - MUTANT A291F


Mass: 13184.946 Da / Num. of mol.: 2 / Fragment: RESIDUES 278-327,229-290 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: THIS STRUCTURE COMPRISES RESIDUES OF THE PROTEIN AF1503 FROM A. FULGIDUS AND THE OSMOLARITY SENSING PROTEIN FROM E. COLI - ONE MUTATION IN POSITION A291F IS INTRODUCED
Source: (gene. exp.) ARCHAEOGLOBUS FULGIDUS (archaea), (gene. exp.) ESCHERICHIA COLI (E. coli)
Strain: VC-16, 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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ALA 291 TO PHE ENGINEERED RESIDUE IN CHAIN B, ALA 291 TO PHE

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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: 36.87 % / Description: NONE
Crystal growpH: 7
Details: 0.1 M TRISODIUM CITRATE PH5.6, 20% PEG4000, 20% ISOPROPANOL, pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.979
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.65→20 Å / Num. obs: 23404 / % possible obs: 99.1 % / Observed criterion σ(I): 2.9 / Redundancy: 6.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.31
Reflection shellResolution: 1.65→1.69 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.9 / % possible all: 91.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.7_650)refinement
XDSdata reduction
XDSdata scaling
SHARPphasing
DMphasing
BUCCANEERmodel building
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.65→23.74 Å / SU ML: 0.2 / σ(F): 1.37 / Phase error: 23.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.24 1154 5 %
Rwork0.196 --
obs0.199 23095 90.6 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.97 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.2281 Å20 Å20 Å2
2---0.1965 Å20 Å2
3----0.0316 Å2
Refinement stepCycle: LAST / Resolution: 1.65→23.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1723 0 0 287 2010
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161932
X-RAY DIFFRACTIONf_angle_d0.7662442
X-RAY DIFFRACTIONf_dihedral_angle_d12.501720
X-RAY DIFFRACTIONf_chiral_restr0.05292
X-RAY DIFFRACTIONf_plane_restr0.004322
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.72510.32621480.26112820X-RAY DIFFRACTION95
1.7251-1.8160.29821560.25312967X-RAY DIFFRACTION100
1.816-1.92980.4079490.2755923X-RAY DIFFRACTION31
1.9298-2.07870.25881570.2252992X-RAY DIFFRACTION100
2.0787-2.28770.23311590.20513010X-RAY DIFFRACTION100
2.2877-2.61840.22851590.18833026X-RAY DIFFRACTION100
2.6184-3.29750.24981600.18533043X-RAY DIFFRACTION100
3.2975-23.74060.21151660.17923160X-RAY DIFFRACTION99
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)
11.5620.142-0.08341.3817-0.1721.2025-0.0030.05890.27220.2670.0090.3398-0.251-0.20520.05930.14690.01310.00930.1101-0.02720.12941.418232.062827.0897
2-0.40080.4817-0.26141.3608-1.44670.6354-0.01510.01470.0677-0.05750.22930.25290.0548-0.03790.07810.23890.01770.03040.180.0270.216-7.15266.455337.8171
31.6378-0.02820.43442.1811-0.90121.86410.13410.10990.01570.4626-0.0542-0.2269-0.33770.17910.05060.11690.04410.01710.16030.01870.1329-1.6049-11.189255.2186
4-0.04710.4122-0.44880.8445-0.75450.3281-0.0793-0.0759-0.0546-0.0850.0148-0.17330.11930.0109-0.06610.14420.0036-0.0020.12380.01690.14998.018911.821529.4136
51.7544-0.02250.71560.4035-0.02820.94860.00970.195-0.2129-0.2094-0.0067-0.11430.3110.309-0.04610.2430.0868-0.00890.3219-0.00620.1547-5.2454-16.9443.6093
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 278:310)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 311:357)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 358:385)
4X-RAY DIFFRACTION4CHAIN B AND (RESSEQ 278:357)
5X-RAY DIFFRACTION5CHAIN B AND (RESSEQ 358:389)

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