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- PDB-9bk4: Crystal structure of RidA family protein PA5083 from Pseudomonas ... -

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Basic information

Entry
Database: PDB / ID: 9bk4
TitleCrystal structure of RidA family protein PA5083 from Pseudomonas aeruginosa with pyruvic acid bound
ComponentsRidA family protein PA5083
KeywordsHYDROLASE / RidA protein / deamination / stress
Function / homologyRutC family, YoaB-like / YjgF/YER057c/UK114 family / Endoribonuclease L-PSP / RutC-like superfamily / PYRUVIC ACID / RidA family protein
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.08 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 RidA family protein PA5083 from Pseudomonas aeruginosa with pyruvic acid 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
A: RidA family protein PA5083
B: RidA family protein PA5083
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4155
Polymers25,1432
Non-polymers2723
Water5,206289
1
A: RidA family protein PA5083
hetero molecules

A: RidA family protein PA5083
hetero molecules

A: RidA family protein PA5083
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2669
Polymers37,7143
Non-polymers5526
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-y+1,x-y+2,z1
crystal symmetry operation3_465-x+y-1,-x+1,z1
Buried area7570 Å2
ΔGint-62 kcal/mol
Surface area13720 Å2
MethodPISA
2
B: RidA family protein PA5083
hetero molecules

B: RidA family protein PA5083
hetero molecules

B: RidA family protein PA5083
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9786
Polymers37,7143
Non-polymers2643
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area7010 Å2
ΔGint-27 kcal/mol
Surface area13600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.404, 75.404, 279.606
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-317-

HOH

21A-321-

HOH

31A-373-

HOH

41A-374-

HOH

51A-418-

HOH

61A-422-

HOH

71A-431-

HOH

81A-441-

HOH

91A-443-

HOH

101B-334-

HOH

111B-335-

HOH

121B-357-

HOH

131B-419-

HOH

141B-428-

HOH

151B-430-

HOH

161B-443-

HOH

171B-444-

HOH

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Components

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


Mass: 12571.302 Da / Num. of mol.: 2
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
Production host: Escherichia coli BL21 (bacteria)
References: UniProt: A0A069Q0R8, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In cyclic amidines
#2: Chemical ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / 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: 3.04 Å3/Da / Density % sol: 59.57 %
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 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.08→50 Å / Num. obs: 18793 / % possible obs: 99.7 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.045 / Χ2: 1.506 / Net I/σ(I): 43.57
Reflection shellResolution: 2.08→2.12 Å / Rmerge(I) obs: 0.143 / Num. unique obs: 911 / CC1/2: 0.984

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Processing

Software
NameVersionClassification
PHENIX(1.21_5207: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.08→47.72 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2185 1879 10 %
Rwork0.1842 --
obs0.1876 18793 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.08→47.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1766 0 17 289 2072
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071806
X-RAY DIFFRACTIONf_angle_d0.8942458
X-RAY DIFFRACTIONf_dihedral_angle_d18.666656
X-RAY DIFFRACTIONf_chiral_restr0.052296
X-RAY DIFFRACTIONf_plane_restr0.006320
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.08-2.130.21081400.17981258X-RAY DIFFRACTION98
2.13-2.20.25951450.18711292X-RAY DIFFRACTION100
2.2-2.270.25121400.18811281X-RAY DIFFRACTION100
2.27-2.350.23841460.19121304X-RAY DIFFRACTION100
2.35-2.440.23811430.17491267X-RAY DIFFRACTION99
2.44-2.550.22181420.18661283X-RAY DIFFRACTION99
2.56-2.690.25031430.19661298X-RAY DIFFRACTION99
2.69-2.860.23451450.17931294X-RAY DIFFRACTION99
2.86-3.080.23691430.19241283X-RAY DIFFRACTION99
3.08-3.390.20161450.1891308X-RAY DIFFRACTION99
3.39-3.880.20521460.17221325X-RAY DIFFRACTION100
3.88-4.890.18731470.16521324X-RAY DIFFRACTION99
4.89-47.720.21481540.20571397X-RAY DIFFRACTION98

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