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- PDB-9bkb: Crystal structure of Rid family protein ACIAD3089 from Acinetobac... -

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Basic information

Entry
Database: PDB / ID: 9bkb
TitleCrystal structure of Rid family protein ACIAD3089 from Acinetobacter baylyi
ComponentsRid family protein ACIAD3089
KeywordsHYDROLASE / Rid family protein / deamination / stress / Endoribonuclease L-PSP/chorismate mutase-like domain-containing protein
Function / homologyEndoribonuclease L-PSP/chorismate mutase-like / YjgF/YER057c/UK114 family / Endoribonuclease L-PSP / RutC-like superfamily / Uncharacterized protein
Function and homology information
Biological speciesAcinetobacter baylyi (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 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 Rid family protein ACIAD3089 from Acinetobacter baylyi
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: Rid family protein ACIAD3089
B: Rid family protein ACIAD3089
C: Rid family protein ACIAD3089


Theoretical massNumber of molelcules
Total (without water)53,3673
Polymers53,3673
Non-polymers00
Water1,892105
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.410, 87.410, 183.680
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11B-203-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 19 or resid 29 through 158))
d_2ens_1chain "B"
d_3ens_1(chain "C" and (resid 1 through 19 or resid 29 through 158))

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11METMETSERSERAA1 - 191 - 19
d_12THRTHRGLNGLNAA29 - 15829 - 158
d_21METMETGLNGLNBB1 - 1581 - 158
d_31METMETSERSERCC1 - 191 - 19
d_32THRTHRGLNGLNCC29 - 15829 - 158

NCS oper:
IDCodeMatrixVector
1given(-0.525750915826, 0.300374299024, -0.795839968206), (-0.274630449094, 0.825540763432, 0.493011728402), (0.805086387252, 0.477763255596, -0.351536883789)-68.3493343488, 0.332944000751, 0.692566302912
2given(-0.492236089103, -0.286808242447, 0.821854405992), (0.322691040495, 0.816760952717, 0.478301200606), (-0.808439314339, 0.500642165805, -0.30948876692)-34.9925522303, 20.9441231811, -54.8352018748

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Components

#1: Protein Rid family protein ACIAD3089


Mass: 17789.084 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baylyi (bacteria) / Gene: ACIAD3089 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q6F828
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 3.29 Å3/Da / Density % sol: 62.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 3350, 0.2M sodium sulfate, Reductive methylation

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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 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→51.28 Å / Num. obs: 68037 / % possible obs: 94.2 % / Redundancy: 11.9 % / Biso Wilson estimate: 42.53 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 21.9
Reflection shellResolution: 2.1→2.4 Å / Rmerge(I) obs: 0.558 / Num. unique obs: 2648

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→51.28 Å / SU ML: 0.2131 / Cross valid method: FREE R-VALUE / σ(F): 1.52 / Phase error: 21.3652
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2217 2000 4.8 %
Rwork0.1986 39706 -
obs0.1997 41706 98.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.54 Å2
Refinement stepCycle: LAST / Resolution: 2.1→51.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3473 0 0 105 3578
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00723517
X-RAY DIFFRACTIONf_angle_d0.93894751
X-RAY DIFFRACTIONf_chiral_restr0.0597565
X-RAY DIFFRACTIONf_plane_restr0.006611
X-RAY DIFFRACTIONf_dihedral_angle_d17.38471271
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS1.20593344647
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.966824532968
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.26951330.22032650X-RAY DIFFRACTION94.21
2.15-2.210.2441380.1982728X-RAY DIFFRACTION95.79
2.21-2.280.20811370.19872714X-RAY DIFFRACTION96.19
2.28-2.350.24691380.20272759X-RAY DIFFRACTION97.21
2.35-2.430.24471420.20292781X-RAY DIFFRACTION97.92
2.43-2.530.26541390.21182785X-RAY DIFFRACTION98.38
2.53-2.650.29241430.23362836X-RAY DIFFRACTION98.71
2.65-2.790.26271430.2232832X-RAY DIFFRACTION99.2
2.79-2.960.24771420.22112841X-RAY DIFFRACTION99.23
2.96-3.190.27041450.23152865X-RAY DIFFRACTION99.77
3.19-3.510.22241460.20892905X-RAY DIFFRACTION99.9
3.51-4.020.19811470.18712914X-RAY DIFFRACTION99.9
4.02-5.060.17511490.16122960X-RAY DIFFRACTION100
5.06-51.280.22081580.20283136X-RAY DIFFRACTION99.88

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