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- PDB-9bjv: Crystal structure of hypothetical protein PA5083 from Pseudomonas... -

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Basic information

Entry
Database: PDB / ID: 9bjv
TitleCrystal structure of hypothetical protein PA5083 from Pseudomonas aeruginosa Sulfur SAD phased
ComponentsRidA family protein PA5083
KeywordsHYDROLASE / Sulfur SAD / Rid 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 / SAD / Resolution: 1.8 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) solved by Sulfur SAD
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

Downloads & links

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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
Water2,450136
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_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area5910 Å2
ΔGint-29 kcal/mol
Surface area14280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.329, 75.329, 139.392
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-223-

HOH

21A-232-

HOH

31A-278-

HOH

41A-293-

HOH

51A-310-

HOH

61A-335-

HOH

71A-336-

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) / Strain: ATCC 15692
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.: 136 / 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: 3.03 Å3/Da / Density % sol: 59.37 %
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: Jul 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 22679 / % possible obs: 97.3 % / Redundancy: 16.6 % / Rmerge(I) obs: 0.033 / Rpim(I) all: 0.008 / Rrim(I) all: 0.034 / Χ2: 0.988 / Net I/σ(I): 87.179
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 4.378 / Num. unique obs: 686 / CC1/2: 0.947 / CC star: 0.986 / Rrim(I) all: 0.35 / Χ2: 0.925 / % possible all: 77.3

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Processing

Software
NameVersionClassification
PHENIX1.21refinement
HKL-3000data scaling
HKL-3000data reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→37.66 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1916 2257 9.95 %
Rwork0.1722 --
obs0.1741 22679 82.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→37.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms883 0 0 136 1019
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007896
X-RAY DIFFRACTIONf_angle_d0.8211220
X-RAY DIFFRACTIONf_dihedral_angle_d17.764327
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 (%)
1.8-1.840.356690.2613617X-RAY DIFFRACTION40
1.84-1.880.2871760.2572688X-RAY DIFFRACTION44
1.88-1.930.245840.213762X-RAY DIFFRACTION49
1.93-1.980.2407940.2006896X-RAY DIFFRACTION59
1.98-2.040.22191150.17261086X-RAY DIFFRACTION69
2.04-2.10.22221450.18711263X-RAY DIFFRACTION83
2.1-2.180.18811600.18471469X-RAY DIFFRACTION95
2.18-2.270.22681730.17961503X-RAY DIFFRACTION99
2.27-2.370.23321680.18261524X-RAY DIFFRACTION98
2.37-2.490.18541640.17651469X-RAY DIFFRACTION97
2.5-2.650.16721700.18231513X-RAY DIFFRACTION97
2.65-2.860.21791660.17641524X-RAY DIFFRACTION99
2.86-3.140.18321620.17071518X-RAY DIFFRACTION98
3.14-3.60.17641670.15621521X-RAY DIFFRACTION98
3.6-4.530.1631740.14391534X-RAY DIFFRACTION100
4.53-37.660.17231700.17311535X-RAY DIFFRACTION99

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