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- PDB-9bka: Crystal structure of Rid family protein PSPTO3006 -

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Basic information

Entry
Database: PDB / ID: 9bka
TitleCrystal structure of Rid family protein PSPTO3006
ComponentsRid family protein PSPTO3006
KeywordsHYDROLASE / Rid family protein / deamination / stress / Deaminase AmnE
Function / homologyYjgF/YER057c/UK114 family / Endoribonuclease L-PSP / RutC-like superfamily / Deaminase AmnE, putative
Function and homology information
Biological speciesPseudomonas syringae pv. tomato (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsZhou, D. / Chen, L. / Rose, J.P. / Wang, B.C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of Rid family protein PSPTO3006
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

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Assembly

Deposited unit
A: Rid family protein PSPTO3006


Theoretical massNumber of molelcules
Total (without water)15,1261
Polymers15,1261
Non-polymers00
Water1,910106
1
A: Rid family protein PSPTO3006

A: Rid family protein PSPTO3006

A: Rid family protein PSPTO3006


Theoretical massNumber of molelcules
Total (without water)45,3783
Polymers45,3783
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_445z-1/2,-x-1/2,-y1
crystal symmetry operation12_455-y-1/2,-z,x+1/21
Buried area5570 Å2
ΔGint-31 kcal/mol
Surface area15540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.307, 71.307, 71.307
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Space group name HallP2ac2ab3
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y+1/2,-z,x+1/2
#5: z+1/2,-x+1/2,-y
#6: -y,z+1/2,-x+1/2
#7: -z+1/2,-x,y+1/2
#8: -z,x+1/2,-y+1/2
#9: y+1/2,-z+1/2,-x
#10: x+1/2,-y+1/2,-z
#11: -x,y+1/2,-z+1/2
#12: -x+1/2,-y,z+1/2
Components on special symmetry positions
IDModelComponents
11A-203-

HOH

21A-295-

HOH

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Components

#1: Protein Rid family protein PSPTO3006


Mass: 15126.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae pv. tomato (bacteria)
Gene: PSPTO_3006 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q880Z0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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 Å3/Da / Density % sol: 38.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.8 M Potassium sodium tartrate tetrahydrate,0.1 M Tris pH 8.5,0.5% w/v Polyethylene glycol monomethyl ether 5,000

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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: Apr 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.86→50 Å / Num. obs: 10209 / % possible obs: 98.1 % / Redundancy: 11.8 % / Biso Wilson estimate: 18.13 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 31.79
Reflection shellResolution: 1.86→1.89 Å / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 2.23 / Num. unique obs: 384

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.86→41.17 Å / SU ML: 0.1705 / Cross valid method: FREE R-VALUE / σ(F): 0.33 / Phase error: 20.3723
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1984 980 9.99 %
Rwork0.1716 8829 -
obs0.1743 9809 94.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.56 Å2
Refinement stepCycle: LAST / Resolution: 1.86→41.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms978 0 0 106 1084
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065998
X-RAY DIFFRACTIONf_angle_d0.8411366
X-RAY DIFFRACTIONf_chiral_restr0.0545165
X-RAY DIFFRACTIONf_plane_restr0.0072181
X-RAY DIFFRACTIONf_dihedral_angle_d14.0359359
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.960.21331080.1941985X-RAY DIFFRACTION74.61
1.96-2.080.22271380.17021245X-RAY DIFFRACTION95.31
2.08-2.240.22631420.16931295X-RAY DIFFRACTION97.96
2.24-2.470.21681450.1721296X-RAY DIFFRACTION97.89
2.47-2.830.22831430.17531293X-RAY DIFFRACTION97.55
2.83-3.560.18531480.17361319X-RAY DIFFRACTION98.19
3.56-41.170.17261560.1661396X-RAY DIFFRACTION99.42

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