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- PDB-3lr4: Periplasmic domain of the risS sensor protein from Burkholderia p... -

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Basic information

Entry
Database: PDB / ID: 3lr4
TitlePeriplasmic domain of the risS sensor protein from Burkholderia pseudomallei, barium phased at low pH
ComponentsSensor protein
KeywordsTRANSFERASE / NIAID / SSGCID / Seattle Structural Genomics Center for Infectious Disease / Burkholderia / melioidosis / pH / sensor / histidine kinase / barium 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 ...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-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / 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
: / 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 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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)15,2128
Polymers14,4541
Non-polymers7587
Water2,594144
1
A: Sensor protein
hetero molecules

A: Sensor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,42416
Polymers28,9092
Non-polymers1,51514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area4500 Å2
ΔGint-145 kcal/mol
Surface area11170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.780, 57.780, 75.900
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Detailsdimeric

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Components

#1: Protein Sensor protein


Mass: 14454.266 Da / Num. of mol.: 1 / Fragment: UNP residues 38 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-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ba
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.53 Å3/Da / Density % sol: 51.39 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: growth: 15% PEG 3350, 0.1 M succinate; soak and cryo-protection: 30% PEG 3350, 0.45 M BaCl2, 0.1 M Na citrate pH 4.5, crystal tracking ID 206692g7, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Feb 4, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNumber: 207365 / Rmerge(I) obs: 0.046 / D res high: 1.9 Å / Num. obs: 22306 / % possible obs: 99.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
8.519.0322088.410.022
6.018.54529810.023
4.916.0159499.810.024
4.254.9170710010.022
3.84.2577710010.024
3.473.888799.910.029
3.213.4794510010.033
33.21103610010.038
2.833109710010.045
2.692.83116610010.06
2.562.69120499.910.062
2.452.56126410010.079
2.362.45134910010.089
2.272.36135599.510.114
2.192.27141999.910.12
2.122.19149299.810.153
2.062.12148410010.178
22.06157410010.229
1.952163499.910.338
1.91.95165099.610.321
ReflectionResolution: 1.9→18.91 Å / Num. obs: 22306 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 9.29 % / Biso Wilson estimate: 28.009 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 33.77
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 4.17 % / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 4.6 / Num. measured obs: 6883 / Num. unique all: 1650 / Num. unique obs: 1650 / % possible all: 99.6

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 1.9 Å / D res low: 19.03 Å / FOM : 0.303 / FOM acentric: 0.335 / FOM centric: 0.097 / Reflection: 11971 / Reflection acentric: 10335 / Reflection centric: 1605
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
8.25-19.030.2770.4250.131618268
6.13-8.250.3430.4480.12523515671
5.09-6.130.4310.5190.13227821563
4.45-5.090.4080.5040.08232525173
4-4.450.4270.5090.08436329370
3.67-40.4510.5340.07239332271
3.41-3.670.4160.4790.09341234567
3.19-3.410.4060.4670.06546039169
3.01-3.190.4370.4990.09348441074
2.86-3.010.3830.430.08749542669
2.73-2.860.4010.4480.10752144972
2.62-2.730.3710.410.08954948365
2.52-2.620.3410.3780.08356649571
2.43-2.520.3580.3950.09559852375
2.35-2.430.3030.3290.10861754671
2.27-2.350.2910.3160.09161955264
2.21-2.270.2610.2840.08865057476
2.14-2.210.2330.2520.09166859371
2.09-2.140.2150.2270.10867660769
2.04-2.090.1910.2010.10470062971
1.99-2.040.1820.1910.10171063773
1.94-1.990.1680.1750.09673066265
1.9-1.940.1450.1470.1276169467

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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→18.91 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.205 / WRfactor Rwork: 0.175 / Occupancy max: 1 / Occupancy min: 0.15 / FOM work R set: 0.843 / SU B: 6.857 / SU ML: 0.091 / SU R Cruickshank DPI: 0.133 / SU Rfree: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.133 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.226 573 4.8 %RANDOM
Rwork0.186 ---
obs0.188 11971 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 66.99 Å2 / Biso mean: 23.72 Å2 / Biso min: 9.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20.19 Å20 Å2
2--0.37 Å20 Å2
3----0.56 Å2
Refinement stepCycle: LAST / Resolution: 1.9→18.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms822 0 7 144 973
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022876
X-RAY DIFFRACTIONr_angle_refined_deg1.3851.9781207
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1435117
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.25324.66745
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.44315150
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.021158
X-RAY DIFFRACTIONr_chiral_restr0.0880.2145
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021676
X-RAY DIFFRACTIONr_mcbond_it0.8051.5541
X-RAY DIFFRACTIONr_mcangle_it1.4962885
X-RAY DIFFRACTIONr_scbond_it2.3453335
X-RAY DIFFRACTIONr_scangle_it3.974.5315
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 38 -
Rwork0.214 826 -
all-864 -
obs--99.65 %
Refinement TLS params.Method: refined / Origin x: 2.6067 Å / Origin y: 25.1925 Å / Origin z: 6.3183 Å
111213212223313233
T0.0347 Å20.0311 Å2-0.009 Å2-0.071 Å2-0.0164 Å2--0.0367 Å2
L1.4825 °2-0.0453 °2-1.2961 °2-0.2224 °20.036 °2--1.1388 °2
S-0.0146 Å °0.0222 Å °-0.0511 Å °-0.006 Å °-0.0409 Å °0.0052 Å °0.002 Å °-0.0331 Å °0.0555 Å °

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