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- PDB-9bjy: Crystal structure of RidA family protein PA5083 from Pseudomonas ... -

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Basic information

Entry
Database: PDB / ID: 9bjy
TitleCrystal structure of RidA family protein PA5083 from Pseudomonas aeruginosa with TMAO bound
ComponentsRidA family protein
KeywordsHYDROLASE / RidA protein / deamination / stress
Function / homologyRutC family, YoaB-like / YjgF/YER057c/UK114 family / Endoribonuclease L-PSP / RutC-like superfamily / trimethylamine oxide / RidA family protein
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsZhou, D. / Chen, L. / Rose, J.P. / Wang, B.C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of the RidA protein PA5083 from Pseudomonas aeruginosa with TMAO bound
Authors: Zhou, D. / Chen, L. / Rose, J.P. / Wang, B.C.
History
DepositionApr 26, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: RidA family protein
A: RidA family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2236
Polymers24,8802
Non-polymers3424
Water7,278404
1
B: RidA family protein
hetero molecules

B: RidA family protein
hetero molecules

B: RidA family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8349
Polymers37,3203
Non-polymers5146
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area7220 Å2
ΔGint-89 kcal/mol
Surface area13370 Å2
MethodPISA
2
A: RidA family protein
hetero molecules

A: RidA family protein
hetero molecules

A: RidA family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8349
Polymers37,3203
Non-polymers5146
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area7000 Å2
ΔGint-93 kcal/mol
Surface area12780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.280, 75.280, 279.505
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Components on special symmetry positions
IDModelComponents
11B-325-

HOH

21B-348-

HOH

31B-351-

HOH

41B-371-

HOH

51B-456-

HOH

61B-468-

HOH

71B-496-

HOH

81B-498-

HOH

91A-342-

HOH

101A-343-

HOH

111A-370-

HOH

121A-447-

HOH

131A-460-

HOH

141A-471-

HOH

151A-498-

HOH

161A-500-

HOH

171A-501-

HOH

181A-504-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1(chain "B" and resid 3 through 115)

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: ARG / End label comp-ID: ARG / Auth seq-ID: 3 - 115 / Label seq-ID: 2 - 114

Dom-IDAuth asym-IDLabel asym-ID
d_1AB
d_2BA

NCS oper: (Code: givenMatrix: (0.992981645483, 0.11825981929, -0.00143766309693), (-0.11825528263, 0.992978956065, 0.00291220563159), (0.00177196611289, -0.00272175548419, 0.999994726078)Vector: -34. ...NCS oper: (Code: given
Matrix: (0.992981645483, 0.11825981929, -0.00143766309693), (-0.11825528263, 0.992978956065, 0.00291220563159), (0.00177196611289, -0.00272175548419, 0.999994726078)
Vector: -34.5217477468, 25.6516800741, -46.0938847261)

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Components

#1: Protein RidA family protein


Mass: 12440.106 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA5083 / Plasmid: pET28 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9HUA0
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-TMO / trimethylamine oxide


Mass: 75.110 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H9NO / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 404 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.03 Å3/Da / Density % sol: 59.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1 M BIS-TRIS pH 5.5, 2.0 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: May 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.58→50 Å / Num. obs: 40206 / % possible obs: 95 % / Redundancy: 3.5 % / Biso Wilson estimate: 14.18 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 19.5
Reflection shellResolution: 1.58→1.61 Å / Rmerge(I) obs: 0.453 / Mean I/σ(I) obs: 2.13 / Num. unique obs: 2915 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.58→47.67 Å / SU ML: 0.1552 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.7996
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2124 1997 4.97 %
Rwork0.1811 38209 -
obs0.1827 40206 94.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.09 Å2
Refinement stepCycle: LAST / Resolution: 1.58→47.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1737 0 20 404 2161
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00861779
X-RAY DIFFRACTIONf_angle_d1.09212426
X-RAY DIFFRACTIONf_chiral_restr0.0591293
X-RAY DIFFRACTIONf_plane_restr0.0096310
X-RAY DIFFRACTIONf_dihedral_angle_d13.4263641
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.635580574694 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.620.28471460.24532769X-RAY DIFFRACTION98.45
1.62-1.660.24171460.22842823X-RAY DIFFRACTION98.83
1.66-1.710.27091480.22292815X-RAY DIFFRACTION98.9
1.71-1.770.24911460.20472821X-RAY DIFFRACTION99.33
1.77-1.830.23771480.21222826X-RAY DIFFRACTION99.23
1.83-1.90.24011470.2012811X-RAY DIFFRACTION98.57
1.9-1.990.19331460.17242792X-RAY DIFFRACTION97.74
1.99-2.10.18481430.16272755X-RAY DIFFRACTION96.06
2.1-2.230.19221410.162676X-RAY DIFFRACTION93.74
2.23-2.40.18441360.15522604X-RAY DIFFRACTION90.52
2.4-2.640.19931340.16812581X-RAY DIFFRACTION89.34
2.64-3.020.21831340.17372551X-RAY DIFFRACTION87.69
3.02-3.810.18841350.16532578X-RAY DIFFRACTION88.23
3.81-47.670.22791470.19222807X-RAY DIFFRACTION91.46

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