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- PDB-3lr0: Periplasmic domain of the risS sensor protein from Burkholderia p... -

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Basic information

Entry
Database: PDB / ID: 3lr0
TitlePeriplasmic domain of the risS sensor protein from Burkholderia pseudomallei, iodide phased at low pH
ComponentsSensor protein
KeywordsTRANSFERASE / NIAID / Seattle Structural Genomics Center for Infectious Disease / SSGCID / pH / sensor protein / risS / iodide phased / Burkholderia / melioidosis / ATP-binding / Kinase / Membrane / Nucleotide-binding / Phosphoprotein / Transmembrane / Two-component regulatory system
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity / membrane
Similarity search - Function
Sensor histidine kinase RisS, periplasmic domain / Sensor histidine kinase RisS, periplasmic domain / Sensor histidine kinase RisS, periplasmic domain superfamily / Periplasmic domain of Sensor histidine kinase RisS / 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 ...Sensor histidine kinase RisS, periplasmic domain / Sensor histidine kinase RisS, periplasmic domain / Sensor histidine kinase RisS, periplasmic domain superfamily / Periplasmic domain of Sensor histidine kinase RisS / 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. / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / histidine kinase
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.9 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Structural basis for pH sensing by the periplasmic domain of the risS histidine kinase from Bukholderia pseudomallei
Authors: Edwards, T.E. / Abendroth, J. / Staker, B.L. / Phan, I. / Myler, P. / Stacy, R. / Stewart, L. / Miller, S.I. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionFeb 10, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sensor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2077
Polymers16,4451
Non-polymers7616
Water1,27971
1
A: Sensor protein
hetero molecules

A: Sensor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,41414
Polymers32,8912
Non-polymers1,52312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area1670 Å2
ΔGint-11 kcal/mol
Surface area10970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.360, 58.360, 75.690
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-46-

GLN

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Components

#1: Protein Sensor protein


Mass: 16445.494 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: 1710b / Gene: BPSL2095 / Production host: Escherichia coli (E. coli) / References: UniProt: Q63T74, histidine kinase
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.26 Å3/Da / Density % sol: 45.64 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: Crystal originally grown in JCSG+ condition a6, 0.1M phosphate-citrate pH 4.2, 0.2 M lithium sulfate, 25% PEG 1000 then soaked and cryo-protected into 0.1 M Na citrate pH 4.5, 1.0 M KI, 30% ...Details: Crystal originally grown in JCSG+ condition a6, 0.1M phosphate-citrate pH 4.2, 0.2 M lithium sulfate, 25% PEG 1000 then soaked and cryo-protected into 0.1 M Na citrate pH 4.5, 1.0 M KI, 30% PEG 1000 for 1 hour prior to vitrification; crystal tracking IDs 203087a6 for growth and 206239a1 for soak; affinity tag not removed prior to crystallization, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Dec 10, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNumber: 89341 / Rmerge(I) obs: 0.046 / D res high: 1.9 Å / Num. obs: 12191 / % possible obs: 99.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
8.519.114789.110.032
6.018.527099.610.033
4.916.0134510010.036
4.254.9140110010.03
3.84.2544610010.032
3.473.849510010.032
3.213.4752910010.039
33.2155510010.044
2.83360410010.054
2.692.8362899.810.065
2.562.6966110010.067
2.452.5666510010.087
2.362.4572710010.09
2.272.3674310010.11
2.192.2777010010.12
2.122.1978810010.148
2.062.1282410010.185
22.0682910010.24
1.95284010010.33
1.91.9592499.910.337
ReflectionResolution: 1.9→19.1 Å / Num. all: 12212 / Num. obs: 12191 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 11.2 % / Biso Wilson estimate: 32.657 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 25.45
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.337 / Mean I/σ(I) obs: 4.1 / Num. measured obs: 4275 / Num. unique all: 925 / Num. unique obs: 924 / % possible all: 99.9

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 2.1 Å / D res low: 19.1 Å / FOM : 0.444 / FOM acentric: 0.486 / FOM centric: 0.203 / Reflection: 9076 / Reflection acentric: 7752 / Reflection centric: 1321
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
8.12-19.10.450.5790.27217510174
6.02-8.120.530.6190.31324517471
5-6.020.4860.560.24730723473
4.36-50.4760.5590.14735128071
3.92-4.360.4870.5650.17838831078
3.59-3.920.5130.5890.14442835573
3.34-3.590.5340.6040.15646439173
3.13-3.340.5180.5830.18948640680
2.95-3.130.5250.5690.2351444767
2.8-2.950.5170.5610.21952345667
2.68-2.80.4910.5290.23258150675
2.56-2.680.470.5120.19760052179
2.47-2.560.4270.4550.22161654472
2.38-2.470.4250.460.16563255775
2.3-2.380.3840.4030.22265258468
2.23-2.30.3630.3880.17368360676
2.16-2.230.3250.3480.15170061981
2.1-2.160.320.3320.21373166168

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.9→19.1 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.914 / WRfactor Rfree: 0.254 / WRfactor Rwork: 0.209 / Occupancy max: 1 / Occupancy min: 0.22 / FOM work R set: 0.839 / SU B: 5.636 / SU ML: 0.089 / SU R Cruickshank DPI: 0.14 / SU Rfree: 0.139 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.254 585 4.8 %RANDOM
Rwork0.211 ---
obs0.213 12191 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 60.93 Å2 / Biso mean: 18.791 Å2 / Biso min: 2.95 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20.23 Å20 Å2
2--0.46 Å20 Å2
3----0.69 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms806 0 6 71 883
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.022875
X-RAY DIFFRACTIONr_angle_refined_deg1.3881.9731204
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9715117
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.79223.33345
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.38515154
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3771511
X-RAY DIFFRACTIONr_chiral_restr0.0890.2143
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021675
X-RAY DIFFRACTIONr_mcbond_it0.8641.5534
X-RAY DIFFRACTIONr_mcangle_it1.5682874
X-RAY DIFFRACTIONr_scbond_it2.4163341
X-RAY DIFFRACTIONr_scangle_it4.0414.5322
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 47 -
Rwork0.216 875 -
all-922 -
obs--99.89 %
Refinement TLS params.Method: refined / Origin x: 2.7336 Å / Origin y: 25.2005 Å / Origin z: 6.1664 Å
111213212223313233
T0.032 Å20.0193 Å20.0014 Å2-0.0652 Å2-0.0218 Å2--0.03 Å2
L3.3633 °2-0.2251 °2-1.9038 °2-0.8835 °2-0.1266 °2--2.2485 °2
S-0.0822 Å °0.0132 Å °-0.1302 Å °-0.0008 Å °-0.0531 Å °0.1125 Å °-0.026 Å °-0.1697 Å °0.1353 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A40 - 141
2X-RAY DIFFRACTION1A1 - 6
3X-RAY DIFFRACTION1A7 - 220

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