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- PDB-8huz: the structure of trans-editing factor ProX -

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Basic information

Entry
Database: PDB / ID: 8huz
Titlethe structure of trans-editing factor ProX
ComponentsProlyl-tRNA synthetase associated domain-containing protein 1
KeywordsTRANSLATION / aminoacylation / editing / tRNA
Function / homologyProlyl-tRNA editing protein ProX/PRXD1 / YbaK/aminoacyl-tRNA synthetase-associated domain / Aminoacyl-tRNA editing domain / YbaK/aminoacyl-tRNA synthetase-associated domain superfamily / aminoacyl-tRNA editing activity / Prolyl-tRNA synthetase associated domain-containing protein 1
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsChen, M. / Zhou, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: the structure of trans-editing factor ProX
Authors: Yuan, C. / Xiao, Y. / Zhou, X. / Chen, M.
History
DepositionDec 25, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: Prolyl-tRNA synthetase associated domain-containing protein 1
A: Prolyl-tRNA synthetase associated domain-containing protein 1
B: Prolyl-tRNA synthetase associated domain-containing protein 1
C: Prolyl-tRNA synthetase associated domain-containing protein 1
D: Prolyl-tRNA synthetase associated domain-containing protein 1
E: Prolyl-tRNA synthetase associated domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)113,3266
Polymers113,3266
Non-polymers00
Water00
1
F: Prolyl-tRNA synthetase associated domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)18,8881
Polymers18,8881
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Prolyl-tRNA synthetase associated domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)18,8881
Polymers18,8881
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Prolyl-tRNA synthetase associated domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)18,8881
Polymers18,8881
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: Prolyl-tRNA synthetase associated domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)18,8881
Polymers18,8881
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
D: Prolyl-tRNA synthetase associated domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)18,8881
Polymers18,8881
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
E: Prolyl-tRNA synthetase associated domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)18,8881
Polymers18,8881
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.802, 94.722, 165.526
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Prolyl-tRNA synthetase associated domain-containing protein 1 / PrdX deacylase domain-containing protein 1


Mass: 18887.732 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Prorsd1, Prdxdd1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9D820

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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 Å3/Da / Density % sol: 59.03 %
Crystal growTemperature: 293 K / Method: evaporation / Details: Ammonium Sulfate, Bis-Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 3.3→47.68 Å / Num. obs: 21079 / % possible obs: 99.49 % / Redundancy: 13.1 % / CC1/2: 1 / Net I/σ(I): 24.4
Reflection shellResolution: 3.3→47.68 Å / Num. unique obs: 21079 / CC1/2: 1

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Processing

Software
NameVersionClassification
PHENIXv3.0refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→47.677 Å / SU ML: 0.61 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 38.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3372 3745 9.48 %
Rwork0.2856 --
obs0.2905 21072 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3→47.677 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7227 0 0 0 7227
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027351
X-RAY DIFFRACTIONf_angle_d0.7079925
X-RAY DIFFRACTIONf_dihedral_angle_d9.7694367
X-RAY DIFFRACTIONf_chiral_restr0.0441136
X-RAY DIFFRACTIONf_plane_restr0.0041290
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3001-3.34180.45381040.39921362X-RAY DIFFRACTION100
3.3418-3.38580.45151520.38251311X-RAY DIFFRACTION99
3.3858-3.43220.38451370.38371270X-RAY DIFFRACTION99
3.4322-3.48120.37431600.35591358X-RAY DIFFRACTION99
3.4812-3.53310.42971600.35271263X-RAY DIFFRACTION99
3.5331-3.58830.37721360.34861364X-RAY DIFFRACTION100
3.5883-3.64710.42581180.33911323X-RAY DIFFRACTION99
3.6471-3.710.38661430.32451284X-RAY DIFFRACTION100
3.71-3.77740.46531380.32911359X-RAY DIFFRACTION100
3.7774-3.850.39591320.3391316X-RAY DIFFRACTION100
3.85-3.92860.40351330.34121348X-RAY DIFFRACTION100
3.9286-4.0140.37791500.32781313X-RAY DIFFRACTION100
4.014-4.10730.35321430.31891327X-RAY DIFFRACTION100
4.1073-4.20990.4391290.31315X-RAY DIFFRACTION100
4.2099-4.32370.3321290.2991352X-RAY DIFFRACTION100
4.3237-4.45080.3471570.29151321X-RAY DIFFRACTION100
4.4508-4.59440.28971350.27341330X-RAY DIFFRACTION100
4.5944-4.75850.31331390.2741315X-RAY DIFFRACTION100
4.7585-4.94880.36441490.27521325X-RAY DIFFRACTION100
4.9488-5.17380.3291290.26211320X-RAY DIFFRACTION100
5.1738-5.44620.28561470.26641334X-RAY DIFFRACTION100
5.4462-5.78680.36371320.27111334X-RAY DIFFRACTION100
5.7868-6.23280.33321410.30591320X-RAY DIFFRACTION100
6.2328-6.85830.35311360.3111324X-RAY DIFFRACTION100
6.8583-7.8470.27641380.27941337X-RAY DIFFRACTION100
7.847-9.87190.28251500.21281315X-RAY DIFFRACTION100
9.8719-47.6770.28211280.24131305X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 15.422 Å / Origin y: -40.8288 Å / Origin z: -19.8033 Å
111213212223313233
T0.8774 Å20.0139 Å20.1351 Å2-0.8498 Å2-0.0567 Å2--0.9112 Å2
L0.6699 °20.1601 °2-0.2437 °2-0.0563 °20.098 °2--0.5827 °2
S0.0737 Å °0.0905 Å °0.082 Å °-0.2745 Å °-0.0456 Å °-0.09 Å °-0.0851 Å °-0.0857 Å °-0.0232 Å °
Refinement TLS groupSelection details: all

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