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

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Basic information

Entry
Database: PDB / ID: 9bjw
TitleCrystal structure of RidA family protein PA5083 from Pseudomonas aeruginosa
ComponentsRidA family protein PA5083
KeywordsHYDROLASE / RidA protein / deamination / stress
Function / homologyRutC family, YoaB-like / YjgF/YER057c/UK114 family / Endoribonuclease L-PSP / RutC-like superfamily / RidA family protein
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 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 Rid protein PA5083 from Pseudomonas aeruginosa (Apo form)
Authors: Zhou, D. / Chen, L. / Rose, J.P. / Wang, B.C.
History
DepositionApr 25, 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: RidA family protein PA5083


Theoretical massNumber of molelcules
Total (without water)12,5711
Polymers12,5711
Non-polymers00
Water2,018112
1
A: RidA family protein PA5083

A: RidA family protein PA5083

A: RidA family protein PA5083


Theoretical massNumber of molelcules
Total (without water)37,7143
Polymers37,7143
Non-polymers00
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 area5890 Å2
ΔGint-32 kcal/mol
Surface area14430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.480, 75.480, 140.040
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-219-

HOH

21A-234-

HOH

31A-250-

HOH

41A-297-

HOH

51A-302-

HOH

61A-305-

HOH

71A-310-

HOH

81A-312-

HOH

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Components

#1: Protein RidA family protein PA5083 / Translation initiation inhibitor


Mass: 12571.302 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: yabJ_3, CAZ10_01035, GNQ48_03865, GUL26_07970, IPC1295_08400, IPC737_05390, NCTC13621_05579, PA52Ts2_0667
Plasmid: pET28 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: A0A069Q0R8, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In cyclic amidines
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 3.05 Å3/Da / Density % sol: 59.72 %
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: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.54→50 Å / Num. obs: 22725 / % possible obs: 99.9 % / Redundancy: 17.2 % / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.015 / Rrim(I) all: 0.063 / Net I/σ(I): 68.87
Reflection shellResolution: 1.54→1.57 Å / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 4.31 / Num. unique obs: 1132 / CC1/2: 0.958 / CC star: 0.989 / Χ2: 0.492 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.21_5207: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.54→37.74 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 0.32 / Phase error: 21.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2128 1988 8.75 %
Rwork0.1982 --
obs0.1995 22725 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.54→37.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms883 0 0 112 995
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007896
X-RAY DIFFRACTIONf_angle_d0.8561220
X-RAY DIFFRACTIONf_dihedral_angle_d18.922327
X-RAY DIFFRACTIONf_chiral_restr0.053148
X-RAY DIFFRACTIONf_plane_restr0.007158
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.580.27331320.23791370X-RAY DIFFRACTION94
1.58-1.620.25441400.21671441X-RAY DIFFRACTION98
1.62-1.670.21431410.22551467X-RAY DIFFRACTION99
1.67-1.720.24681380.22261471X-RAY DIFFRACTION99
1.73-1.790.26921400.22951462X-RAY DIFFRACTION99
1.79-1.860.25851420.22141470X-RAY DIFFRACTION100
1.86-1.940.21611440.20511497X-RAY DIFFRACTION99
1.94-2.040.22441410.19541472X-RAY DIFFRACTION100
2.05-2.170.19881410.19481473X-RAY DIFFRACTION99
2.17-2.340.1951450.20821505X-RAY DIFFRACTION100
2.34-2.580.20961430.19721494X-RAY DIFFRACTION100
2.58-2.950.19581430.20151499X-RAY DIFFRACTION100
2.95-3.710.20221460.18891529X-RAY DIFFRACTION100
3.72-37.740.21091520.18291587X-RAY DIFFRACTION100

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