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- PDB-3zcc: High resolution structure of the asymmetric R333G Hamp-Dhp mutant -

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Basic information

Entry
Database: PDB / ID: 3zcc
TitleHigh resolution structure of the asymmetric R333G Hamp-Dhp mutant
ComponentsHAMP, OSMOLARITY SENSOR PROTEIN ENVZ
KeywordsSIGNALING PROTEIN / SIGNAL TRANSDUCTION / MEMBRANE PROTEIN / SIGNALLING / CHIMERA
Function / homology
Function and homology information


response to osmotic stress / histidine kinase / phosphorelay sensor kinase activity / phosphoprotein phosphatase activity / phosphorelay signal transduction system / outer membrane-bounded periplasmic space / protein autophosphorylation / phosphorylation / signal transduction / protein homodimerization activity ...response to osmotic stress / histidine kinase / phosphorelay sensor kinase activity / phosphoprotein phosphatase activity / phosphorelay signal transduction system / outer membrane-bounded periplasmic space / protein autophosphorylation / phosphorylation / signal transduction / protein homodimerization activity / ATP binding / membrane / identical protein binding / 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 K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsZeth, K. / Muench, C. / Ferris, H.
CitationJournal: To be Published
Title: Structure of Mutant of Hamp-Dhp Fusion
Authors: Zeth, K. / Muench, C. / Ferris, H.
History
DepositionNov 19, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2013Group: Atomic model / Other
Revision 1.2Mar 15, 2017Group: Source and taxonomy

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)25,5012
Polymers25,5012
Non-polymers00
Water4,612256
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-52.9 kcal/mol
Surface area12280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.060, 57.460, 52.340
Angle α, β, γ (deg.)90.00, 107.84, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 12750.410 Da / Num. of mol.: 2 / Fragment: RESIDUES 278-327,229-288 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARCHAEOGLOBUS FULGIDUS (archaea), (gene. exp.) ESCHERICHIA COLI K-12 (bacteria)
Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: O28769, UniProt: P0AEJ4, histidine kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.02 Å3/Da / Density % sol: 39.23 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.25→37 Å / Num. obs: 52485 / % possible obs: 93.3 % / Observed criterion σ(I): 1.8 / Redundancy: 3.7 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 14.6
Reflection shellResolution: 1.25→1.33 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 1.77 / % possible all: 77.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.1_1168)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3YRX

3yrx


Resolution: 1.25→37.643 Å / SU ML: 0.14 / σ(F): 1.4 / Phase error: 23.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2039 2624 5 %
Rwork0.1895 --
obs0.1903 52464 93.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.25→37.643 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1722 0 0 256 1978
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091756
X-RAY DIFFRACTIONf_angle_d1.3122376
X-RAY DIFFRACTIONf_dihedral_angle_d12.716690
X-RAY DIFFRACTIONf_chiral_restr0.066284
X-RAY DIFFRACTIONf_plane_restr0.006314
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2503-1.2730.3832940.34251778X-RAY DIFFRACTION64
1.273-1.29750.27551120.31252139X-RAY DIFFRACTION76
1.2975-1.3240.29061340.29072538X-RAY DIFFRACTION91
1.324-1.35280.28921390.27112634X-RAY DIFFRACTION94
1.3528-1.38420.28161400.26342673X-RAY DIFFRACTION95
1.3842-1.41890.28841390.2582633X-RAY DIFFRACTION95
1.4189-1.45720.27551410.2392677X-RAY DIFFRACTION95
1.4572-1.50010.25941400.20962662X-RAY DIFFRACTION95
1.5001-1.54850.20321410.20142687X-RAY DIFFRACTION96
1.5485-1.60390.23051430.19512700X-RAY DIFFRACTION97
1.6039-1.66810.20261420.19052703X-RAY DIFFRACTION96
1.6681-1.7440.23151440.19232742X-RAY DIFFRACTION97
1.744-1.8360.21871420.18182704X-RAY DIFFRACTION97
1.836-1.9510.21271450.18012744X-RAY DIFFRACTION98
1.951-2.10160.18581450.1732748X-RAY DIFFRACTION98
2.1016-2.31310.18761450.15012759X-RAY DIFFRACTION98
2.3131-2.64770.161460.16082772X-RAY DIFFRACTION98
2.6477-3.33550.15671470.17072797X-RAY DIFFRACTION98
3.3355-37.65970.20761450.19492750X-RAY DIFFRACTION95
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)
12.48690.34020.80552.38760.00343.2042-0.0045-0.04270.12950.1486-0.0329-0.2536-0.25340.13550.01560.1363-0.0257-0.00810.07330.0010.104114.5547.14235.2868
26.6297-1.58284.39290.703-1.25933.0677-0.07520.20280.36680.0846-0.1089-0.058-0.04870.13030.18760.0934-0.01020.0170.077-0.00980.1109-1.17239.7044-15.578
36.373-0.97243.43720.9887-0.85793.2609-0.0524-0.32590.18720.07240.0414-0.11660.0033-0.14590.01350.10040.00350.00120.0718-0.03450.115-23.008914.1521-19.0735
41.686-0.41450.2563.1363-0.01713.78480.06380.0096-0.0410.1346-0.0336-0.06520.1321-0.0505-0.02370.0629-0.00740.0130.0615-0.01660.065610.4246-5.6191.4941
51.6603-0.54741.00931.2801-0.67031.77020.11730.1033-0.1053-0.2037-0.0629-0.1160.23770.1064-0.0530.1305-0.00180.01330.0681-0.01920.1011-20.94296.3949-27.3826
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 278 THROUGH 310 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 311 THROUGH 357 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 358 THROUGH 387 )
4X-RAY DIFFRACTION4CHAIN B AND (RESID 278 THROUGH 334 )
5X-RAY DIFFRACTION5CHAIN B AND (RESID 335 THROUGH 387 )

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