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- PDB-9bk8: Crystal structure of RidA family protein PA5083 from Pseudomonas ... -

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Basic information

Entry
Database: PDB / ID: 9bk8
TitleCrystal structure of RidA family protein PA5083 from Pseudomonas aeruginosa with 2-ketobutyric 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 / 2-KETOBUTYRIC ACID / RidA family protein
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.67 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 2-ketobutyric 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

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Assembly

Deposited unit
A: RidA family protein PA5083
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6732
Polymers12,5711
Non-polymers1021
Water2,162120
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)38,0206
Polymers37,7143
Non-polymers3063
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 area7060 Å2
ΔGint-24 kcal/mol
Surface area13660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.547, 75.547, 139.748
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3
Components on special symmetry positions
IDModelComponents
11A-307-

HOH

21A-323-

HOH

31A-343-

HOH

41A-398-

HOH

51A-405-

HOH

61A-416-

HOH

71A-418-

HOH

81A-420-

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
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-2KT / 2-KETOBUTYRIC ACID / 2-OXOBUTANOIC ACID


Mass: 102.089 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 3.05 Å3/Da / Density % sol: 59.71 %
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: Jun 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.67→50 Å / Num. obs: 17998 / % possible obs: 99.4 % / Redundancy: 6.2 % / Biso Wilson estimate: 17.86 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 36.43
Reflection shellResolution: 1.67→1.7 Å / Rmerge(I) obs: 0.424 / Num. unique obs: 789 / CC1/2: 0.872 / % possible all: 89.1

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.67→37.77 Å / SU ML: 0.1675 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.2934
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1952 1802 10.01 %
Rwork0.1818 16196 -
obs0.1832 17998 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.74 Å2
Refinement stepCycle: LAST / Resolution: 1.67→37.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms883 0 7 120 1010
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009902
X-RAY DIFFRACTIONf_angle_d1.02961227
X-RAY DIFFRACTIONf_chiral_restr0.058148
X-RAY DIFFRACTIONf_plane_restr0.0103160
X-RAY DIFFRACTIONf_dihedral_angle_d16.318329
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.67-1.720.2981320.24581199X-RAY DIFFRACTION96.8
1.72-1.770.22871380.2181247X-RAY DIFFRACTION100
1.77-1.820.22631380.20011234X-RAY DIFFRACTION99.93
1.82-1.890.21961350.20421222X-RAY DIFFRACTION99.71
1.89-1.960.20421360.18061224X-RAY DIFFRACTION99.56
1.96-2.050.22981400.17461257X-RAY DIFFRACTION99.64
2.05-2.160.19271370.17631224X-RAY DIFFRACTION99.71
2.16-2.30.19961380.18551248X-RAY DIFFRACTION99.43
2.3-2.470.19151390.1751246X-RAY DIFFRACTION99.5
2.47-2.720.18221380.17271236X-RAY DIFFRACTION99.49
2.72-3.120.18961410.17041257X-RAY DIFFRACTION99.08
3.12-3.930.1781420.15981272X-RAY DIFFRACTION99.51
3.93-37.770.18281480.19651330X-RAY DIFFRACTION99.46

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