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

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Basic information

Entry
Database: PDB / ID: 9bkh
TitleCrystal structure of RidA family protein PA5083 from Pseudomonas aeruginosa with Acetaldehyde 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 / ACETYL GROUP / 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 Acetaldehyde bound
Authors: Zhou, D. / Chen, L. / Rose, J.P. / Wang, B.C.
History
DepositionApr 28, 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)12,6152
Polymers12,5711
Non-polymers441
Water1,78399
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)37,8466
Polymers37,7143
Non-polymers1323
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 area6660 Å2
ΔGint-36 kcal/mol
Surface area13670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.332, 75.332, 139.794
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-305-

HOH

21A-326-

HOH

31A-328-

HOH

41A-339-

HOH

51A-389-

HOH

61A-396-

HOH

71A-399-

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(DE3) (bacteria)
References: UniProt: A0A069Q0R8, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In cyclic amidines
#2: Chemical ChemComp-ACE / ACETYL GROUP


Mass: 44.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 59.49 %
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 28, 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: 17900 / % possible obs: 99.3 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 35.6
Reflection shellResolution: 1.67→1.7 Å / Rmerge(I) obs: 0.545 / Num. unique obs: 783

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Processing

Software
NameVersionClassification
PHENIX(1.21_5207: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.67→37.67 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2131 1782 10 %
Rwork0.1873 --
obs0.1898 17819 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.67→37.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms880 0 3 99 982
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009895
X-RAY DIFFRACTIONf_angle_d1.061217
X-RAY DIFFRACTIONf_dihedral_angle_d16.961325
X-RAY DIFFRACTIONf_chiral_restr0.059148
X-RAY DIFFRACTIONf_plane_restr0.012157
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.67-1.720.26581300.2391168X-RAY DIFFRACTION95
1.72-1.770.24061340.22031203X-RAY DIFFRACTION98
1.77-1.820.22961360.21051222X-RAY DIFFRACTION99
1.82-1.890.25261320.22071210X-RAY DIFFRACTION100
1.89-1.970.27911350.18671209X-RAY DIFFRACTION100
1.97-2.050.21461390.18531255X-RAY DIFFRACTION100
2.05-2.160.23931360.17781213X-RAY DIFFRACTION100
2.16-2.30.21511390.1881253X-RAY DIFFRACTION100
2.3-2.480.191350.18861221X-RAY DIFFRACTION100
2.48-2.720.19311380.1761248X-RAY DIFFRACTION99
2.73-3.120.21211390.1841248X-RAY DIFFRACTION99
3.12-3.930.17361410.16891256X-RAY DIFFRACTION100
3.93-37.670.22491480.19341331X-RAY DIFFRACTION100

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