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- PDB-9bk9: Crystal structure of Rid family protein PA0814 from Pseudomonas a... -

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Basic information

Entry
Database: PDB / ID: 9bk9
TitleCrystal structure of Rid family protein PA0814 from Pseudomonas aeruginosa
ComponentsRid family protein PA0814
KeywordsHYDROLASE / Rid family protein / deamination / stress
Function / homologyEndoribonuclease L-PSP/chorismate mutase-like / YjgF/YER057c/UK114 family / Endoribonuclease L-PSP / RutC-like superfamily / Uncharacterized protein
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 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 PA0814 from Pseudomonas aeruginosa
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 PA0814
B: Rid family protein PA0814
C: Rid family protein PA0814
D: Rid family protein PA0814
E: Rid family protein PA0814
F: Rid family protein PA0814


Theoretical massNumber of molelcules
Total (without water)89,5566
Polymers89,5566
Non-polymers00
Water8,917495
1
A: Rid family protein PA0814
B: Rid family protein PA0814
C: Rid family protein PA0814


Theoretical massNumber of molelcules
Total (without water)44,7783
Polymers44,7783
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Rid family protein PA0814
F: Rid family protein PA0814

D: Rid family protein PA0814


Theoretical massNumber of molelcules
Total (without water)44,7783
Polymers44,7783
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y+1/2,-z+11
Unit cell
Length a, b, c (Å)46.970, 84.647, 85.789
Angle α, β, γ (deg.)90.000, 90.710, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 15 through 143)
d_2ens_1(chain "B" and resid 15 through 143)
d_3ens_1(chain "C" and resid 15 through 143)
d_4ens_1(chain "D" and resid 15 through 143)
d_5ens_1(chain "E" and resid 15 through 143)
d_6ens_1(chain "F" and resid 15 through 143)

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: TYR / Beg label comp-ID: TYR / End auth comp-ID: ARG / End label comp-ID: ARG / Auth seq-ID: 15 - 143 / Label seq-ID: 15 - 143

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB
d_3CC
d_4DD
d_5EE
d_6FF

NCS oper:
IDCodeMatrixVector
1given(0.623081583666, 0.219254624135, -0.750797409353), (-0.603239558655, -0.47630115535, -0.639718097513), (-0.497866824532, 0.851507263156, -0.164511415481)0.0583322079762, 18.9586190903, -5.60471930552
2given(0.612831914528, -0.6150638745, -0.496118408065), (0.232333053672, -0.459835448707, 0.857072174489), (-0.755286963152, -0.640505886309, -0.138902170233)8.48147549536, 13.7007524782, 11.3167482097
3given(0.872715265374, -0.0657517352684, -0.483781743034), (-0.149457004707, -0.979299052927, -0.136513620862), (-0.464790995317, 0.191442091104, -0.864476290263)21.7429141532, 1.11997576434, 42.1562113038
4given(-0.822332917051, 0.187278855435, 0.537303642125), (0.568413441283, 0.31348204542, 0.76068072604), (-0.0259756290208, 0.930943412623, -0.364238423551)22.4275221636, 25.7292750346, 35.1546701646
5given(-0.898631973465, 0.196573708957, 0.392198104551), (-0.18798680207, 0.635217337092, -0.749106065191), (-0.396385593223, -0.746898729149, -0.533873346292)23.0141950909, 27.3486813954, 55.0451491894

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Components

#1: Protein
Rid family protein PA0814


Mass: 14926.070 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA0814 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9I5C5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 495 / 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: 1.9 Å3/Da / Density % sol: 35.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium acetate, 0.1 M Sodium acetate trihydrate pH 4.6,30% w/v Polyethylene glycol 4,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 62539 / % possible obs: 97.4 % / Redundancy: 7.7 % / Biso Wilson estimate: 17.28 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 35.13
Reflection shellResolution: 1.78→1.81 Å / Rmerge(I) obs: 0.941 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 3070 / CC1/2: 0.877 / Χ2: 0.823

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→37.96 Å / SU ML: 0.1672 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.1151
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2146 1988 3.18 %
Rwork0.1877 60495 -
obs0.1885 62483 97.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.14 Å2
Refinement stepCycle: LAST / Resolution: 1.78→37.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5817 0 0 495 6312
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00715906
X-RAY DIFFRACTIONf_angle_d1.02458017
X-RAY DIFFRACTIONf_chiral_restr0.0592922
X-RAY DIFFRACTIONf_plane_restr0.0081064
X-RAY DIFFRACTIONf_dihedral_angle_d18.12612116
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS1.02006006675
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS1.10057216623
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.967214957715
ens_1d_5AAX-RAY DIFFRACTIONTorsion NCS0.962959839384
ens_1d_6AAX-RAY DIFFRACTIONTorsion NCS0.810511454217
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.820.26221400.23694144X-RAY DIFFRACTION92.99
1.82-1.870.25291410.22514235X-RAY DIFFRACTION96.05
1.87-1.930.24891490.21464246X-RAY DIFFRACTION96.23
1.93-1.990.25561290.20594242X-RAY DIFFRACTION96.13
1.99-2.060.2371340.20444319X-RAY DIFFRACTION96.85
2.06-2.150.25571390.19834317X-RAY DIFFRACTION96.89
2.15-2.240.23191510.19474288X-RAY DIFFRACTION97.28
2.24-2.360.21561460.1934333X-RAY DIFFRACTION97.43
2.36-2.510.23131460.1914309X-RAY DIFFRACTION97.7
2.51-2.70.25221380.20334360X-RAY DIFFRACTION98.04
2.7-2.970.20221560.19564356X-RAY DIFFRACTION98.17
2.97-3.40.19141380.18144420X-RAY DIFFRACTION98.72
3.4-4.290.17791380.15964441X-RAY DIFFRACTION98.9
4.29-37.960.19161430.17164485X-RAY DIFFRACTION98.87

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