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- PDB-3lr5: Periplasmic domain of the risS sensor protein from Burkholderia p... -

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Basic information

Entry
Database: PDB / ID: 3lr5
TitlePeriplasmic domain of the risS sensor protein from Burkholderia pseudomallei, iodide phased at neutral pH
ComponentsSensor protein
KeywordsTRANSFERASE / NIAID / SSGCID / Seattle Structural Genomics Center for Infectious Disease / Burkholderia / melioidosis / pH / sensor protein / histidine kinase / iodide phased / 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: 2.3 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Structural basis for pH sensing by the periplsamic domain of the risS histidine kinase from Burkholderia 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: 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 / 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
B: Sensor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7007
Polymers33,0652
Non-polymers6355
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-10 kcal/mol
Surface area14670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.040, 76.010, 88.680
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsdimeric

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Components

#1: Protein Sensor protein


Mass: 16532.572 Da / Num. of mol.: 2 / Fragment: UNP residues 37 to 158
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.: 5 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.14 Å3/Da / Density % sol: 42.59 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M BisTris Propane pH 6.5, 0.2 M NaI, 25% PEG 3350, crystal tracking ID 203088f3, 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: Jan 4, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNumber: 90482 / Rmerge(I) obs: 0.084 / D res high: 2.25 Å / Num. obs: 25375 / % possible obs: 97.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
10.0619.7525787.110.029
7.1210.0652899.410.036
5.817.1268099.710.048
5.035.8182810010.045
4.55.0392199.910.039
4.114.5101999.910.04
3.84.11107397.410.05
3.563.8109990.410.07
3.353.56124999.110.067
3.183.35135810010.075
3.033.18140810010.092
2.93.03149510010.106
2.792.9153510010.136
2.692.79162210010.155
2.62.69164610010.181
2.522.6173010010.207
2.442.52175210010.236
2.372.44185899.910.277
2.312.37187699.810.344
2.252.31144174.410.433
ReflectionResolution: 2.3→19.61 Å / Num. obs: 13048 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 6.69 % / Biso Wilson estimate: 30.555 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 15.79
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 6.25 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 4.6 / Num. measured obs: 5916 / Num. unique all: 949 / Num. unique obs: 947 / % possible all: 99.8

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 2.5 Å / D res low: 19.75 Å / FOM : 0.386 / FOM acentric: 0.429 / FOM centric: 0.164 / Reflection: 10217 / Reflection acentric: 8564 / Reflection centric: 1626
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
9.79-19.750.3860.5920.1261789977
7.39-9.790.4120.5390.14925116781
6.18-7.390.4820.5860.20930021683
5.42-6.180.490.5740.22734426083
4.88-5.420.4330.5040.17738630383
4.48-4.880.460.5370.14641933781
4.16-4.480.4040.4710.12244435885
3.91-4.160.4180.4750.14246238474
3.69-3.910.3930.4420.15947239472
3.51-3.690.3620.4070.14248040271
3.35-3.510.390.4380.13956047089
3.21-3.350.4180.4590.16558149982
3.09-3.210.40.4370.16760051783
2.98-3.090.390.4270.14961453183
2.88-2.980.3650.3940.17764755889
2.79-2.880.3560.3810.17565357479
2.71-2.790.3590.390.14568159586
2.63-2.710.3530.3740.1868961574
2.56-2.630.3220.3370.21673464193
2.5-2.560.3240.3440.15372264478

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.3→19.61 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.897 / WRfactor Rfree: 0.226 / WRfactor Rwork: 0.184 / Occupancy max: 1 / Occupancy min: 0.27 / FOM work R set: 0.83 / SU B: 12.228 / SU ML: 0.156 / SU R Cruickshank DPI: 0.352 / SU Rfree: 0.245 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.352 / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.252 640 4.9 %RANDOM
Rwork0.203 ---
obs0.206 13048 98.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 53.31 Å2 / Biso mean: 22.722 Å2 / Biso min: 6.95 Å2
Baniso -1Baniso -2Baniso -3
1-0.89 Å20 Å20 Å2
2---1.64 Å20 Å2
3---0.75 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1928 0 5 163 2096
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0211996
X-RAY DIFFRACTIONr_angle_refined_deg1.5041.9562727
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7195249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.13623.551107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.19715331
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8391523
X-RAY DIFFRACTIONr_chiral_restr0.10.2316
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211550
X-RAY DIFFRACTIONr_mcbond_it0.7751.51226
X-RAY DIFFRACTIONr_mcangle_it1.45221988
X-RAY DIFFRACTIONr_scbond_it2.1563770
X-RAY DIFFRACTIONr_scangle_it3.5784.5734
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 47 -
Rwork0.198 898 -
all-945 -
obs--99.79 %
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)
11.27850.3233-0.11460.9078-0.2433-0.0989-0.00830.0807-0.11690.03120.0248-0.017-0.0277-0.0188-0.01650.02-0.00970.00030.0627-0.00610.02730.364840.184517.5849
20.18170.1253-0.11720.4925-0.75411.32570.0737-0.02160.04270.0225-0.00730.0813-0.0395-0.0023-0.06640.0330.00540.00970.0323-0.00650.05215.770446.237834.5005
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999

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