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- PDB-5guq: Crystal structure of ASCH from Zymomonas mobilis -

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Basic information

Entry
Database: PDB / ID: 5guq
TitleCrystal structure of ASCH from Zymomonas mobilis
ComponentsHelix-turn-helix domain-containing protein
KeywordsHYDROLASE / nuclease
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 / Resolution: 1.697 Å
AuthorsHa, S.C. / Park, S.Y. / Kim, J.S.
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 30, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)69,2154
Polymers69,2154
Non-polymers00
Water13,151730
1
A: Helix-turn-helix domain-containing protein


Theoretical massNumber of molelcules
Total (without water)17,3041
Polymers17,3041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Helix-turn-helix domain-containing protein


Theoretical massNumber of molelcules
Total (without water)17,3041
Polymers17,3041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Helix-turn-helix domain-containing protein


Theoretical massNumber of molelcules
Total (without water)17,3041
Polymers17,3041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Helix-turn-helix domain-containing protein


Theoretical massNumber of molelcules
Total (without water)17,3041
Polymers17,3041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.910, 52.859, 88.675
Angle α, β, γ (deg.)90.00, 111.56, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Helix-turn-helix domain-containing protein / ASCH-domain containing protein


Mass: 17303.820 Da / Num. of mol.: 4
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.: 730 / 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: 2.3 Å3/Da / Density % sol: 46.56 %
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: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 31, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.697→30.6 Å / Num. obs: 68764 / % possible obs: 98.7 % / Redundancy: 3.4 % / Net I/σ(I): 17.6
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.5 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 1.697→30.592 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.72
RfactorNum. reflection% reflection
Rfree0.2354 2751 4 %
Rwork0.1979 --
obs0.1994 68764 98.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.697→30.592 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4766 0 0 730 5496
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074960
X-RAY DIFFRACTIONf_angle_d1.2646739
X-RAY DIFFRACTIONf_dihedral_angle_d15.7931895
X-RAY DIFFRACTIONf_chiral_restr0.085739
X-RAY DIFFRACTIONf_plane_restr0.008864
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6972-1.72640.31541340.26053052X-RAY DIFFRACTION93
1.7264-1.75780.30391310.24843293X-RAY DIFFRACTION99
1.7578-1.79160.28281320.23393291X-RAY DIFFRACTION99
1.7916-1.82820.29851420.23053318X-RAY DIFFRACTION99
1.8282-1.8680.24671360.22083311X-RAY DIFFRACTION99
1.868-1.91140.29511340.21843301X-RAY DIFFRACTION99
1.9114-1.95920.22891400.20743296X-RAY DIFFRACTION99
1.9592-2.01220.26681350.2053292X-RAY DIFFRACTION99
2.0122-2.07140.25641450.19753283X-RAY DIFFRACTION99
2.0714-2.13820.22421300.19813334X-RAY DIFFRACTION99
2.1382-2.21460.23051430.19883308X-RAY DIFFRACTION99
2.2146-2.30320.2491420.2013317X-RAY DIFFRACTION99
2.3032-2.4080.2521290.20523302X-RAY DIFFRACTION99
2.408-2.53490.25351470.20483321X-RAY DIFFRACTION99
2.5349-2.69370.2231380.20343326X-RAY DIFFRACTION100
2.6937-2.90150.24711380.20383334X-RAY DIFFRACTION99
2.9015-3.19320.22891370.20043362X-RAY DIFFRACTION100
3.1932-3.65460.20841350.17573357X-RAY DIFFRACTION99
3.6546-4.60190.20281400.16863252X-RAY DIFFRACTION96
4.6019-30.59660.23141430.20423363X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -32.7342 Å / Origin y: -4.2284 Å / Origin z: -19.5975 Å
111213212223313233
T0.2549 Å20.0046 Å2-0.0453 Å2-0.0975 Å2-0.0116 Å2--0.1514 Å2
L0.435 °20.0428 °20.222 °2-0.1343 °2-0.0147 °2--0.2078 °2
S0.0284 Å °-0.0055 Å °-0.0143 Å °0.0873 Å °-0.0161 Å °-0.0283 Å °0.029 Å °0.0199 Å °-0.0104 Å °
Refinement TLS groupSelection details: all

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