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- PDB-4mn5: Crystal structure of PAS domain of S. aureus YycG -

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Basic information

Entry
Database: PDB / ID: 4mn5
TitleCrystal structure of PAS domain of S. aureus YycG
ComponentsSensor protein kinase WalK
KeywordsTRANSFERASE / PAS domain / histidine kinase
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain / PAS-associated, C-terminal / PAS domain / PAC domain profile. / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain ...HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain / PAS-associated, C-terminal / PAS domain / PAC domain profile. / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / PAS domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Beta-Lactamase / PAS domain / PAS repeat profile. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain / PAS domain superfamily / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Sensor protein kinase WalK
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsShaikh, N. / Hvorup, R. / Winnen, B. / Collins, B.M. / King, G.F.
CitationJournal: To be Published
Title: Crystal structure of PAS domain of S. aureus YycG
Authors: Shaikh, N. / Hvorup, R. / Winnen, B. / Collins, B.M. / King, G.F.
History
DepositionSep 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sensor protein kinase WalK
B: Sensor protein kinase WalK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7904
Polymers29,6602
Non-polymers1312
Water1,36976
1
A: Sensor protein kinase WalK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8952
Polymers14,8301
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sensor protein kinase WalK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8952
Polymers14,8301
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-13 kcal/mol
Surface area11390 Å2
MethodPISA
4
A: Sensor protein kinase WalK
hetero molecules

B: Sensor protein kinase WalK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7904
Polymers29,6602
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x+1/2,-y+3/2,-z1
Buried area1350 Å2
ΔGint-14 kcal/mol
Surface area11770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.820, 60.510, 84.500
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 Sensor protein kinase WalK /


Mass: 14829.815 Da / Num. of mol.: 2 / Fragment: UNP residues 58-183
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: vicK, walK, yycG / Plasmid: pGEX2T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9RDT3, histidine kinase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.54 Å3/Da / Density % sol: 51.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100 mM Tris (pH 8.0), 20 mM ZnCl2, 20% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 12, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→42.25 Å / Num. obs: 20961 / % possible obs: 99.7 % / Observed criterion σ(I): 2.5 / Redundancy: 9.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.8
Reflection shellResolution: 2→2.11 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.742 / Mean I/σ(I) obs: 2.5 / % possible all: 99.7

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SOLVEphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2→34.641 Å / SU ML: 0.52 / σ(F): 1.34 / Phase error: 26.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2527 1072 5.13 %RANDOM
Rwork0.2205 ---
obs0.2221 20907 99.51 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.775 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-8.2057 Å20 Å2-0 Å2
2--6.741 Å20 Å2
3----14.9467 Å2
Refinement stepCycle: LAST / Resolution: 2→34.641 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1614 0 2 76 1692
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081646
X-RAY DIFFRACTIONf_angle_d1.072217
X-RAY DIFFRACTIONf_dihedral_angle_d15.976621
X-RAY DIFFRACTIONf_chiral_restr0.069267
X-RAY DIFFRACTIONf_plane_restr0.003281
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.0910.3571460.28682432X-RAY DIFFRACTION100
2.091-2.20130.26591340.25952419X-RAY DIFFRACTION100
2.2013-2.33920.28771400.22632459X-RAY DIFFRACTION100
2.3392-2.51970.29341380.23652439X-RAY DIFFRACTION100
2.5197-2.77320.24131290.22772467X-RAY DIFFRACTION100
2.7732-3.17420.26391160.2252503X-RAY DIFFRACTION100
3.1742-3.99830.22571410.21212526X-RAY DIFFRACTION100
3.9983-34.64650.24721280.20912590X-RAY DIFFRACTION98

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