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- PDB-4y2f: CRYSTAL STRUCTURE OF NATIVE GAF DOMAIN of POTASSIUM SENSOR HISTID... -

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Basic information

Entry
Database: PDB / ID: 4y2f
TitleCRYSTAL STRUCTURE OF NATIVE GAF DOMAIN of POTASSIUM SENSOR HISTIDINE KINASE KDPD FROM ESCHERICHIA COLI
ComponentsSensor protein KdpD
KeywordsTRANSFERASE / GAF-domain
Function / homology
Function and homology information


transferase activity, transferring phosphorus-containing groups / cellular response to potassium ion / histidine kinase / phosphorelay sensor kinase activity / outer membrane-bounded periplasmic space / signal transduction / protein homodimerization activity / ATP binding / plasma membrane / cytosol
Similarity search - Function
Signal transduction histidine kinase, osmosensitive K+ channel sensor, N-terminal / Sensor protein KdpD, transmembrane domain / KdpD, transmembrane domain superfamily / Osmosensitive K+ channel His kinase sensor domain / Domain of unknown function (DUF4118) / GAF domain / GAF domain / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain ...Signal transduction histidine kinase, osmosensitive K+ channel sensor, N-terminal / Sensor protein KdpD, transmembrane domain / KdpD, transmembrane domain superfamily / Osmosensitive K+ channel His kinase sensor domain / Domain of unknown function (DUF4118) / GAF domain / GAF 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. / GAF domain / GAF-like domain superfamily / Beta-Lactamase / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.396 Å
AuthorsKumar, S. / Yernool, D.A.
CitationJournal: To Be Published
Title: CRYSTAL STRUCTURE OF NATIVE GAF DOMAIN of POTASSIUM SENSOR HISTIDINE KINASE KDPD FROM ESCHERICHIA COLI
Authors: Kumar, S. / Yernool, D.A.
History
DepositionFeb 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sensor protein KdpD


Theoretical massNumber of molelcules
Total (without water)16,3271
Polymers16,3271
Non-polymers00
Water3,117173
1
A: Sensor protein KdpD

A: Sensor protein KdpD


Theoretical massNumber of molelcules
Total (without water)32,6532
Polymers32,6532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area1750 Å2
ΔGint-13 kcal/mol
Surface area14320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.250, 57.540, 61.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-873-

HOH

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Components

#1: Protein Sensor protein KdpD


Mass: 16326.551 Da / Num. of mol.: 1 / Fragment: GAF domain (UNP residues 515-646)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: kdpD, b0695, JW0683 / Production host: Escherichia coli (E. coli) / References: UniProt: P21865, histidine kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 1.79 Å3/Da / Density % sol: 31.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 30-35% PEG 3350, 0.1 M Bis-TRIS pH 6.0 - 6.5 / PH range: 6.0 - 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 0.97932 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 1.39→28.77 Å / Num. obs: 24876 / % possible obs: 98.3 % / Redundancy: 14.1 % / Rsym value: 0.73 / Net I/σ(I): 18
Reflection shellResolution: 1.396→1.446 Å / Redundancy: 13.9 % / Rsym value: 1.96 / % possible all: 97.1

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Processing

Software
NameVersionClassification
PHENIX(dev-2313_1839: ???)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.396→30.058 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 20.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2048 1983 7.97 %Random
Rwork0.1811 ---
obs0.183 24874 97.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.396→30.058 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1085 0 0 173 1258
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061118
X-RAY DIFFRACTIONf_angle_d0.8861525
X-RAY DIFFRACTIONf_dihedral_angle_d13.665415
X-RAY DIFFRACTIONf_chiral_restr0.071176
X-RAY DIFFRACTIONf_plane_restr0.006200
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.396-1.43090.4151350.33661571X-RAY DIFFRACTION97
1.4309-1.46960.28841370.2891610X-RAY DIFFRACTION96
1.4696-1.51290.28861350.24021572X-RAY DIFFRACTION98
1.5129-1.56170.23261420.20831605X-RAY DIFFRACTION98
1.5617-1.61750.24961360.21271581X-RAY DIFFRACTION97
1.6175-1.68230.21711380.20441629X-RAY DIFFRACTION97
1.6823-1.75880.23121420.19471598X-RAY DIFFRACTION98
1.7588-1.85150.21271410.18241649X-RAY DIFFRACTION98
1.8515-1.96750.20731440.17941609X-RAY DIFFRACTION98
1.9675-2.11940.21381400.17321658X-RAY DIFFRACTION99
2.1194-2.33260.22211490.17171671X-RAY DIFFRACTION99
2.3326-2.66990.21351440.17091666X-RAY DIFFRACTION99
2.6699-3.36310.16571490.16481688X-RAY DIFFRACTION100
3.3631-30.0650.18331510.17141784X-RAY DIFFRACTION98
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)
12.86820.32420.78671.26581.97057.1699-0.3681-0.10330.20460.4748-0.10760.5238-0.17420.14060.27070.2980.03050.06560.1546-0.02390.24966.125226.960244.734
23.6771-0.09581.37533.5299-0.48997.50940.0283-0.6252-0.19560.6227-0.05290.10150.3387-0.1887-0.14030.2409-0.00710.03250.2010.02770.11167.971112.043850.2291
37.2789-5.60823.83426.3402-3.9023.5505-0.0338-0.3304-0.25410.04060.5778-0.162-0.1471-0.9717-0.49280.2269-0.0181-0.03490.27930.01670.26082.15566.256444.1325
41.9341-0.489-0.82295.46240.76646.0121-0.0573-0.2398-0.15250.34910.0246-0.25260.30730.27980.05420.1310.0222-0.02590.16220.02690.183817.60356.384443.8744
51.6313-0.38780.92543.21681.38793.5781-0.0093-0.0520.00580.15170.0648-0.24680.01160.1105-0.04620.10470.00380.00770.11410.0090.118214.283112.480242.5572
64.38556.1274-4.24358.707-6.00584.35280.06740.4535-0.2585-0.30960.1034-0.07920.4441-0.2677-0.21460.17020.0015-0.0040.19-0.0190.14398.904114.438727.9467
71.3892-0.3911-0.22283.06740.49432.0506-0.0383-0.26050.02010.56520.0676-0.2013-0.28650.15010.00170.1830.0065-0.03630.15270.00280.121515.27423.364346.2481
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -3 through 543 )
2X-RAY DIFFRACTION2chain 'A' and (resid 544 through 560 )
3X-RAY DIFFRACTION3chain 'A' and (resid 561 through 571 )
4X-RAY DIFFRACTION4chain 'A' and (resid 572 through 591 )
5X-RAY DIFFRACTION5chain 'A' and (resid 592 through 616 )
6X-RAY DIFFRACTION6chain 'A' and (resid 617 through 624 )
7X-RAY DIFFRACTION7chain 'A' and (resid 625 through 653 )

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