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- PDB-5b1n: DHp domain structure of EnvZ from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 5b1n
TitleDHp domain structure of EnvZ from Escherichia coli
ComponentsOsmolarity sensor protein EnvZ
KeywordsSIGNALING PROTEIN / Two-component system / Autophosphorylation / DHp domain / Histidine kinase
Function / homology
Function and homology information


response to osmotic stress / histidine kinase / phosphorelay sensor kinase activity / phosphorelay signal transduction system / phosphoprotein phosphatase activity / outer membrane-bounded periplasmic space / protein autophosphorylation / signal transduction / protein homodimerization activity / ATP binding ...response to osmotic stress / histidine kinase / phosphorelay sensor kinase activity / phosphorelay signal transduction system / phosphoprotein phosphatase activity / outer membrane-bounded periplasmic space / protein autophosphorylation / signal transduction / protein homodimerization activity / ATP 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-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-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 / Histidine kinase/HSP90-like ATPase superfamily / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Sensor histidine kinase EnvZ
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsOkajima, T. / Eguchi, Y. / Tochio, N. / Inukai, Y. / Shimizu, R. / Ueda, S. / Shinya, S. / Kigawa, T. / Fukamizo, T. / Igarashi, M. / Utsumi, R.
CitationJournal: J. Antibiot. / Year: 2017
Title: Angucycline antibiotic waldiomycin recognizes common structural motif conserved in bacterial histidine kinases
Authors: Eguchi, Y. / Okajima, T. / Tochio, N. / Inukai, Y. / Shimizu, R. / Ueda, S. / Shinya, S. / Kigawa, T. / Fukamizo, T. / Igarashi, M. / Utsumi, R.
History
DepositionDec 9, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2017Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Osmolarity sensor protein EnvZ


Theoretical massNumber of molelcules
Total (without water)7,7221
Polymers7,7221
Non-polymers00
Water1,65792
1
A: Osmolarity sensor protein EnvZ

A: Osmolarity sensor protein EnvZ


Theoretical massNumber of molelcules
Total (without water)15,4442
Polymers15,4442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
Buried area2550 Å2
ΔGint-31 kcal/mol
Surface area7370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.510, 38.510, 84.508
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62

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Components

#1: Protein Osmolarity sensor protein EnvZ


Mass: 7721.801 Da / Num. of mol.: 1 / Fragment: DHp domain, UNP residues 223-289
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: envZ / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0K5ZMN4, UniProt: P0AEJ4*PLUS, histidine kinase, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a nitrogenous group as acceptor
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.34 Å3/Da / Density % sol: 47.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.9 / Details: 1.1-1.3 M sodium/potassium phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jul 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.2→42.258 Å / Num. all: 15966 / Num. obs: 15966 / % possible obs: 97.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 17.08 Å2 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.022 / Rrim(I) all: 0.057 / Rsym value: 0.052 / Net I/av σ(I): 8.249 / Net I/σ(I): 18.1 / Num. measured all: 104426
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.33-1.46.50.4181.81523423550.1760.4184.5100
1.4-1.496.60.2632.61479122520.1110.2636.9100
1.49-1.596.60.1723.81389921180.0740.17211.4100
1.59-1.726.60.1135.71296319630.0480.11316.6100
1.72-1.886.70.0856.91207118060.0360.08521.4100
1.88-2.16.70.087.31102716490.0330.0826.8100
2.1-2.436.70.0599.8976314560.0240.05932.2100
2.43-2.976.70.03815.8820112250.0160.03833.399.8
2.97-4.215.80.0321.246127930.0140.0331.282.9
4.21-42.2585.30.0322.318653490.0140.0328.565.3

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Processing

Software
NameVersionClassification
MOSFLMdata processing
SCALA3.2.25data scaling
SCALAdata reduction
PHASER2.5.5phasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZRX

3zrx


Resolution: 1.33→19.255 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 22.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2106 817 5.14 %Random selection
Rwork0.1766 15087 --
obs0.1784 15904 97.67 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.9 Å2 / Biso mean: 30.1073 Å2 / Biso min: 14.73 Å2
Refinement stepCycle: final / Resolution: 1.33→19.255 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms472 0 0 92 564
Biso mean---45.03 -
Num. residues----59
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016488
X-RAY DIFFRACTIONf_angle_d1.623658
X-RAY DIFFRACTIONf_chiral_restr0.0776
X-RAY DIFFRACTIONf_plane_restr0.00987
X-RAY DIFFRACTIONf_dihedral_angle_d14.214191
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3302-1.41350.251390.21542554X-RAY DIFFRACTION100
1.4135-1.52260.23051390.19172551X-RAY DIFFRACTION99
1.5226-1.67570.21441330.17322579X-RAY DIFFRACTION100
1.6757-1.9180.2011250.18052585X-RAY DIFFRACTION100
1.918-2.41570.19711520.17652556X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 10.3423 Å / Origin y: 22.1493 Å / Origin z: -0.1481 Å
111213212223313233
T0.1253 Å20.033 Å20.0031 Å2-0.0968 Å20.0054 Å2--0.1961 Å2
L2.5784 °2-0.3843 °20.1373 °2-1.5465 °2-0.6642 °2--4.904 °2
S0.0965 Å °0.1145 Å °0.1425 Å °-0.1728 Å °-0.1784 Å °-0.044 Å °-0.2228 Å °0.1106 Å °0.0714 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA231 - 289
2X-RAY DIFFRACTION1allS301 - 392

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