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- PDB-9bkc: Crystal structure of Rid family protein PFL1385 from Pseudomonas ... -

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Basic information

Entry
Database: PDB / ID: 9bkc
TitleCrystal structure of Rid family protein PFL1385 from Pseudomonas fluorescens
ComponentsRid family protein PFL1385
KeywordsHYDROLASE / Rid family protein / deamination / stress / Endoribonuclease L-PSP family protein
Function / homologydeaminase activity / YjgF/YER057c/UK114 family / Endoribonuclease L-PSP / RutC-like superfamily / cytosol / Endoribonuclease L-PSP family protein
Function and homology information
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 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 PFL1385 from Pseudomonas fluorescens
Authors: Zhou, D. / Chen, L. / Rose, J.P. / Wang, B.C.
History
DepositionApr 27, 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 PFL1385
B: Rid family protein PFL1385
C: Rid family protein PFL1385
D: Rid family protein PFL1385
E: Rid family protein PFL1385
F: Rid family protein PFL1385


Theoretical massNumber of molelcules
Total (without water)104,7006
Polymers104,7006
Non-polymers00
Water1,838102
1
A: Rid family protein PFL1385
B: Rid family protein PFL1385
C: Rid family protein PFL1385


Theoretical massNumber of molelcules
Total (without water)52,3503
Polymers52,3503
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Rid family protein PFL1385
F: Rid family protein PFL1385

D: Rid family protein PFL1385


Theoretical massNumber of molelcules
Total (without water)52,3503
Polymers52,3503
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565y,-x+1,z+1/41
Unit cell
Length a, b, c (Å)84.010, 84.010, 123.780
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Space group name HallP4cw
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: -x,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 39 through 164)
d_2ens_1(chain "B" and resid 39 through 164)
d_3ens_1chain "C"
d_4ens_1chain "D"
d_5ens_1chain "E"
d_6ens_1(chain "F" and resid 39 through 164)

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ALA / End label comp-ID: ALA / Auth seq-ID: 39 - 164 / Label seq-ID: 39 - 164

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

NCS oper:
IDCodeMatrixVector
1given(-0.185234498037, 0.0811270206877, -0.979339873206), (-0.976315879304, 0.0981705490659, 0.19279483166), (0.111783203371, 0.991857323313, 0.0610210261598)39.7874967003, 26.5820496932, 2.91515145878
2given(-0.180163635126, -0.975802512048, 0.123897223778), (0.060406136608, 0.114744670343, 0.991556735284), (-0.981780099227, 0.186126618487, 0.0382716429249)32.3239330227, -8.54269138931, 33.8869213223
3given(0.936051469082, -0.351388301945, 0.0182731630006), (-0.351048121491, -0.936155771589, -0.0194316164666), (0.0239345697225, 0.0117742335951, -0.999644188597)41.8730737539, 42.1258774958, 31.6683880361
4given(0.0130336442011, 0.236268926904, -0.971600287309), (0.172048941801, 0.956661095089, 0.234944058808), (0.985002175502, -0.170224978554, -0.0281810385197)37.8849249981, 9.20237668853, 28.6613312627
5given(0.967379466316, -0.178746103934, 0.179518239962), (-0.187872735186, -0.0308227227056, 0.981709628729), (-0.169943530399, -0.983412319474, -0.0633987884912)3.47270479262, 14.4543848379, 61.6452581162

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Components

#1: Protein
Rid family protein PFL1385


Mass: 17450.025 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Gene: PFL_1385 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q4KGW9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.09 Å3/Da / Density % sol: 41.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris pH 8.5, 1.5 M Ammonium sulfate

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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: Aug 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.49→50 Å / Num. obs: 29451 / % possible obs: 100 % / Redundancy: 11.46 % / Biso Wilson estimate: 60.65 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 23.36
Reflection shellResolution: 2.49→2.55 Å / Redundancy: 11.59 % / Rmerge(I) obs: 0.541 / Mean I/σ(I) obs: 4.42 / Num. unique obs: 1987 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.49→37.57 Å / SU ML: 0.306 / Cross valid method: FREE R-VALUE / σ(F): 0.07 / Phase error: 26.3691
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2391 1986 6.74 %
Rwork0.1974 27465 -
obs0.2002 29451 97.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.22 Å2
Refinement stepCycle: LAST / Resolution: 2.49→37.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5701 0 0 102 5803
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00835785
X-RAY DIFFRACTIONf_angle_d1.13187876
X-RAY DIFFRACTIONf_chiral_restr0.0618965
X-RAY DIFFRACTIONf_plane_restr0.00821030
X-RAY DIFFRACTIONf_dihedral_angle_d16.42032148
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS1.09973900922
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS1.12878158265
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS1.14268314157
ens_1d_5AAX-RAY DIFFRACTIONTorsion NCS0.980384672449
ens_1d_6AAX-RAY DIFFRACTIONTorsion NCS0.850491686975
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.49-2.550.32951320.23781855X-RAY DIFFRACTION92.55
2.55-2.620.25741320.22211845X-RAY DIFFRACTION92.77
2.62-2.70.32161330.23261890X-RAY DIFFRACTION95.07
2.7-2.790.29931400.24521932X-RAY DIFFRACTION96.64
2.79-2.880.31460.22531959X-RAY DIFFRACTION97.54
2.89-30.27551430.21611966X-RAY DIFFRACTION98.69
3-3.140.28511450.2161965X-RAY DIFFRACTION99.11
3.14-3.30.25541470.21922024X-RAY DIFFRACTION99.68
3.3-3.510.25531470.20451963X-RAY DIFFRACTION99.72
3.51-3.780.23881420.20061984X-RAY DIFFRACTION99.58
3.78-4.160.23191440.18452029X-RAY DIFFRACTION99.95
4.16-4.760.22491470.18011993X-RAY DIFFRACTION100
4.76-5.990.21781430.19562023X-RAY DIFFRACTION100
5.99-37.570.20251450.17932037X-RAY DIFFRACTION99.73

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