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- PDB-3jyb: Crystal Structure of the RetS periplasmic domain -

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Basic information

Entry
Database: PDB / ID: 3jyb
TitleCrystal Structure of the RetS periplasmic domain
ComponentsSensor protein
KeywordsTRANSFERASE / BETA BARREL / carbohydrate binding domain / signaling kinase / two component system / RetS / Kinase / Phosphoprotein
Function / homology
Function and homology information


cellular hyperosmotic response / histidine kinase / phosphorelay sensor kinase activity / membrane
Similarity search - Function
Immunoglobulin-like - #2380 / 7TM-DISM receptor, extracellular domain, type 2 / 7TM-DISM receptor, extracellular domain, type 1 / 7TM diverse intracellular signalling / 7TMR-DISM extracellular 2 / 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 ...Immunoglobulin-like - #2380 / 7TM-DISM receptor, extracellular domain, type 2 / 7TM-DISM receptor, extracellular domain, type 1 / 7TM diverse intracellular signalling / 7TMR-DISM extracellular 2 / 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. / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Histidine kinase / histidine kinase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.04 Å
AuthorsJing, X. / Schubot, F.D. / Robinson, H.
CitationJournal: Proteins / Year: 2010
Title: Crystal structure and oligomeric state of the RetS signaling kinase sensory domain.
Authors: Jing, X. / Jaw, J. / Robinson, H.H. / Schubot, F.D.
History
DepositionSep 21, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sensor protein
B: Sensor protein


Theoretical massNumber of molelcules
Total (without water)34,0542
Polymers34,0542
Non-polymers00
Water1,874104
1
A: Sensor protein


Theoretical massNumber of molelcules
Total (without water)17,0271
Polymers17,0271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sensor protein


Theoretical massNumber of molelcules
Total (without water)17,0271
Polymers17,0271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.164, 67.193, 86.214
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 /


Mass: 17026.943 Da / Num. of mol.: 2 / Fragment: periplasmic domain (UNP 41-185)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: UCBPP-PA14 / Gene: PA14_64230, PA4856, retS, rets (AMINO ACIDS 41 - 185) / Plasmid: HisMBPpDEST / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)codonplus RIL
References: UniProt: Q9HUV7, UniProt: A0A0H2ZI10*PLUS, histidine kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.18 Å3/Da / Density % sol: 43.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 3
Details: 22.5% PEG 3350, 0.1M citric acid, 10% glycerol, pH 3.0, VAPOR DIFFUSION, SITTING DROP, temperature 291.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 20, 2008 / Details: SAGITALLY FOCUSED Si(111)
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.04→30 Å / Num. all: 19459 / Num. obs: 19459 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 13.1 % / Biso Wilson estimate: 18.747 Å2 / Rmerge(I) obs: 0.114 / Rsym value: 0.114 / Net I/σ(I): 26.32
Reflection shellResolution: 2.04→2.11 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 4.65 / Rsym value: 0.444 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.2.0019phasing
HKL-2000data collection
RefinementMethod to determine structure: SAD / Resolution: 2.04→29.62 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.922 / SU B: 8.563 / SU ML: 0.121 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.224 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23491 975 5.2 %RANDOM
Rwork0.19937 ---
obs0.20119 17870 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.747 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å20 Å2
2--0.35 Å20 Å2
3----0.03 Å2
Refine analyzeLuzzati coordinate error obs: 0.224 Å
Refinement stepCycle: LAST / Resolution: 2.04→29.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2298 0 0 104 2402
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222368
X-RAY DIFFRACTIONr_angle_refined_deg1.1191.9563224
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2815274
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.18122.951122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.14315392
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4251524
X-RAY DIFFRACTIONr_chiral_restr0.0720.2336
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021854
X-RAY DIFFRACTIONr_nbd_refined0.1880.2974
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21559
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.2127
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1280.28
X-RAY DIFFRACTIONr_mcbond_it0.5131.51439
X-RAY DIFFRACTIONr_mcangle_it0.74322260
X-RAY DIFFRACTIONr_scbond_it1.07631091
X-RAY DIFFRACTIONr_scangle_it1.8354.5964
LS refinement shellResolution: 2.044→2.097 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 57 -
Rwork0.207 1208 -
obs--100 %
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)
10.74090.3338-0.42470.8253-0.47091.6439-0.0279-0.03010.02050.0473-0.0215-0.0166-0.0011-0.0020.0494-0.03960.0058-0.0022-0.03370.0047-0.02336.911548.398361.5405
21.28750.81670.67781.66120.56370.98930.0644-0.0253-0.14960.01620.0085-0.08750.0943-0.0035-0.0728-0.03410.0023-0.0068-0.0346-0.002-0.0307-6.912131.81941.8151
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A48 - 145
2X-RAY DIFFRACTION2B48 - 145

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