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- PDB-5y6b: Crystal structure of ZmASCH Y47F mutant protein from Zymomonas mobilis -

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Basic information

Entry
Database: PDB / ID: 5y6b
TitleCrystal structure of ZmASCH Y47F mutant protein from Zymomonas mobilis
ComponentsHelix-turn-helix domain-containing protein
KeywordsRNA BINDING PROTEIN / RNA cleavage activity
Function / homologyASCH domain / ASCH domain / exonuclease activity / PUA-like superfamily / endonuclease activity / Hydrolases; Acting on ester bonds / DNA binding / RNA binding / ASCH domain-containing ribonuclease
Function and homology information
Biological speciesZymomonas mobilis subsp. mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPark, S.-Y. / Kim, J.-S.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (Korea)2014R1A2A2A01004915 Korea, Republic Of
National Research Foundation (Korea)2014R1A4A1003642 Korea, Republic Of
CitationJournal: Sci Rep / Year: 2017
Title: Crystal structure of an ASCH protein from Zymomonas mobilis and its ribonuclease activity specific for single-stranded RNA.
Authors: Kim, B.N. / Shin, M. / Ha, S.C. / Park, S.Y. / Seo, P.W. / Hofmann, A. / Kim, J.S.
History
DepositionAug 11, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Helix-turn-helix domain-containing protein
B: Helix-turn-helix domain-containing protein
C: Helix-turn-helix domain-containing protein
D: Helix-turn-helix domain-containing protein


Theoretical massNumber of molelcules
Total (without water)69,2074
Polymers69,2074
Non-polymers00
Water6,431357
1
A: Helix-turn-helix domain-containing protein


Theoretical massNumber of molelcules
Total (without water)17,3021
Polymers17,3021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Helix-turn-helix domain-containing protein


Theoretical massNumber of molelcules
Total (without water)17,3021
Polymers17,3021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Helix-turn-helix domain-containing protein


Theoretical massNumber of molelcules
Total (without water)17,3021
Polymers17,3021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Helix-turn-helix domain-containing protein


Theoretical massNumber of molelcules
Total (without water)17,3021
Polymers17,3021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.126, 65.963, 91.857
Angle α, β, γ (deg.)90.000, 90.180, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Helix-turn-helix domain-containing protein / Activating signal cointegrator-1 homology protein


Mass: 17301.846 Da / Num. of mol.: 4 / Mutation: Y47F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zymomonas mobilis subsp. mobilis (strain ATCC 10988 / DSM 424 / LMG 404 / NCIMB 8938 / NRRL B-806 / ZM1) (bacteria)
Strain: ATCC 10988 / DSM 424 / LMG 404 / NCIMB 8938 / NRRL B-806 / ZM1
Gene: Zmob_0380 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H3G0N3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / 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: 2.39 Å3/Da / Density % sol: 48.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% (w/v) PEG 3350, 0.1M MES (pH 6.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 41869 / % possible obs: 97.6 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.054 / Rrim(I) all: 0.093 / Χ2: 0.919 / Net I/σ(I): 7.8 / Num. measured all: 116741
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.032.60.46920940.7460.3530.590.65297.4
2.03-2.072.50.37720200.850.2830.4740.696
2.07-2.112.90.39721280.8250.2830.4890.68199
2.11-2.152.90.36120840.8610.2560.4440.76998.8
2.15-2.22.90.31721070.9110.2270.3920.82998.6
2.2-2.252.80.27220860.9120.1970.3370.94198.2
2.25-2.312.80.21621150.9450.1540.2660.74598.5
2.31-2.372.80.19320590.9530.140.240.78498
2.37-2.442.70.18521110.9490.1360.230.81897.7
2.44-2.522.60.14920430.9680.1120.1880.95395.7
2.52-2.612.90.14420970.9660.1030.1780.99998.5
2.61-2.712.90.12821080.9730.0910.1571.06597.8
2.71-2.842.90.11221120.9810.080.1381.03498.3
2.84-2.992.80.09220910.9850.0670.1141.07397.9
2.99-3.172.70.0820760.9860.0590.11.01797.3
3.17-3.422.80.07120840.9880.0510.0881.04696.4
3.42-3.762.90.06121200.9910.0430.0751.09398.4
3.76-4.32.90.05521150.9930.0380.0671.08697.8
4.3-5.392.70.05120900.9940.0360.0621.03495.9
5.39-202.80.05221290.9950.0360.0641.05896.3

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GUQ, 5GUS

5guq

5gus


Resolution: 2→19.842 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 30.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2541 1989 4.75 %
Rwork0.2218 39842 -
obs0.2233 41831 97.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.06 Å2 / Biso mean: 31.0161 Å2 / Biso min: 12.57 Å2
Refinement stepCycle: final / Resolution: 2→19.842 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4667 0 0 357 5024
Biso mean---31.05 -
Num. residues----566
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094808
X-RAY DIFFRACTIONf_angle_d0.9936519
X-RAY DIFFRACTIONf_chiral_restr0.057714
X-RAY DIFFRACTIONf_plane_restr0.006832
X-RAY DIFFRACTIONf_dihedral_angle_d17.7782923
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0002-2.05020.38491360.31982661279791
2.0502-2.10550.30351410.29312812295399
2.1055-2.16740.32551490.29382906305599
2.1674-2.23730.37471430.27222843298698
2.2373-2.31710.28741440.26112898304299
2.3171-2.40980.32981370.26132872300998
2.4098-2.51920.2921360.25322764290096
2.5192-2.65180.26421450.24662898304398
2.6518-2.81750.25661440.24322848299298
2.8175-3.03430.29771390.23762871301098
3.0343-3.33840.24231410.21932819296097
3.3384-3.81840.20871460.20122912305898
3.8184-4.79950.22061450.17542825297096
4.7995-19.84290.2251430.19732913305697

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