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- PDB-5y6c: Crystal structure of ZmASCH S128A mutant protein from Zymomonas m... -

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Basic information

Entry
Database: PDB / ID: 5y6c
TitleCrystal structure of ZmASCH S128A 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: 2.398 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7466
Polymers34,6042
Non-polymers1424
Water1,56787
1
A: Helix-turn-helix domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4084
Polymers17,3021
Non-polymers1063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8120 Å2
MethodPISA
2
B: Helix-turn-helix domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3372
Polymers17,3021
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-9 kcal/mol
Surface area7980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.149, 52.149, 207.461
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-337-

HOH

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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.: 2 / Mutation: S128A
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: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.48 Å3/Da / Density % sol: 50.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 800mM Sodium phosphate monobasic/1200mM Potassium phosphate dibasic, 100mM Sodium acetate/Acetic acid pH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 13604 / % possible obs: 99.8 % / Redundancy: 9.3 % / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.025 / Rrim(I) all: 0.077 / Χ2: 1.049 / Net I/σ(I): 33.6 / Num. measured all: 126205
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.4490.1146620.9880.040.1210.98699.7
2.44-2.4990.1066630.9920.0370.1121.05599.8
2.49-2.539.20.16380.9880.0350.1061.06799.8
2.53-2.589.10.1026700.9870.0360.1091.046100
2.58-2.649.20.096580.9950.0310.0961.02299.7
2.64-2.79.10.0876680.9950.030.0921.038100
2.7-2.779.10.0876770.9940.030.0931.093100
2.77-2.849.20.0846590.9960.0290.0891.003100
2.84-2.939.40.086760.9940.0280.0841.022100
2.93-3.029.30.0736730.9960.0250.0781.037100
3.02-3.139.60.0696670.9960.0240.0731.008100
3.13-3.259.40.076880.9970.0240.0741.085100
3.25-3.49.80.0626580.9970.0210.0651.117100
3.4-3.589.70.0676800.9970.0230.0711.017100
3.58-3.89.60.0626910.9970.0210.0661.136100
3.8-4.099.60.0646900.9970.0220.0681.104100
4.09-4.59.40.0776930.9970.0270.0821.053100
4.5-5.149.40.0857070.9940.030.090.998100
5.14-6.449.40.0637270.9970.0220.0671.044100
6.44-208.10.0557590.9950.0210.0591.04497.3

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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: 2.398→19.834 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2354 1346 9.93 %
Rwork0.2058 12204 -
obs0.2088 13550 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.77 Å2 / Biso mean: 26.1215 Å2 / Biso min: 7.18 Å2
Refinement stepCycle: final / Resolution: 2.398→19.834 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2340 0 4 87 2431
Biso mean--42.46 26.38 -
Num. residues----284
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.022389
X-RAY DIFFRACTIONf_angle_d1.663240
X-RAY DIFFRACTIONf_chiral_restr0.11353
X-RAY DIFFRACTIONf_plane_restr0.01414
X-RAY DIFFRACTIONf_dihedral_angle_d26.158906
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3975-2.4830.31661320.25041182131499
2.483-2.58230.30751340.23511741308100
2.5823-2.69950.23111330.235211911324100
2.6995-2.84150.24291330.223711941327100
2.8415-3.01890.28271330.243512201353100
3.0189-3.25110.26091330.218112161349100
3.2511-3.57650.21621310.201212031334100
3.5765-4.09010.21721360.179212451381100
4.0901-5.13820.18341390.15812561395100
5.1382-19.83480.2221420.21431323146599

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