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- PDB-6l7m: Characterization and structural analysis of a thermostable zearal... -

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Basic information

Entry
Database: PDB / ID: 6l7m
TitleCharacterization and structural analysis of a thermostable zearalenone-degrading enzyme
ComponentsAB hydrolase-1 domain-containing protein
KeywordsHYDROLASE / mycotoxin / ZEN-degrading enzyme ZhdF / thermostablity
Function / homologyalpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / AB hydrolase-1 domain-containing protein
Function and homology information
Biological speciesMonosporascus sp. MG133 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsWei, X.H. / Meng, G.
CitationJournal: To Be published
Title: Characterization and structural analysis of a thermostable zearalenone-degrading enzyme
Authors: Wei, X.H. / Meng, G.
History
DepositionNov 1, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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: AB hydrolase-1 domain-containing protein
B: AB hydrolase-1 domain-containing protein
C: AB hydrolase-1 domain-containing protein
D: AB hydrolase-1 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)119,2284
Polymers119,2284
Non-polymers00
Water10,431579
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.010, 116.320, 130.190
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
AB hydrolase-1 domain-containing protein / ZhdF


Mass: 29807.023 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Monosporascus sp. MG133 (fungus) / Gene: DL767_010056 / Production host: Escherichia coli 042 (bacteria) / References: UniProt: A0A4Q4UBE4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 579 / 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: 3.05 Å3/Da / Density % sol: 59.65 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 20% PEG 3350 and 0.2 M Potassium fluoride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 16, 2019
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 57727 / % possible obs: 100 % / Redundancy: 12.3 % / Biso Wilson estimate: 20.93 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.105 / Rrim(I) all: 0.268 / Χ2: 1.01 / Net I/av σ(I): 12.8 / Net I/σ(I): 12.8
Reflection shellResolution: 2.4→2.47 Å / Redundancy: 13 % / Rmerge(I) obs: 0.733 / Mean I/σ(I) obs: 5.9 / Num. unique obs: 4442 / Rpim(I) all: 0.657 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMACccp4 7.0.077refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XO6

5xo6


Resolution: 2.4→49.794 Å / Cor.coef. Fo:Fc: 0.868 / Cor.coef. Fo:Fc free: 0.844 / SU B: 0.001 / SU ML: 0 / Cross valid method: NONE / ESU R: 0.245 / ESU R Free: 0.272
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2753 2975 5.162 %
Rwork0.2483 --
all0.25 --
obs-57634 99.913 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.931 Å2
Baniso -1Baniso -2Baniso -3
1--0.067 Å20 Å20 Å2
2--0.937 Å2-0 Å2
3----0.87 Å2
Refinement stepCycle: LAST / Resolution: 2.4→49.794 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8368 0 0 579 8947
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.4620.3212240.2423982X-RAY DIFFRACTION100
2.462-2.5290.3042120.2433888X-RAY DIFFRACTION100
2.529-2.6030.2492020.233769X-RAY DIFFRACTION100
2.603-2.6820.2791980.2323653X-RAY DIFFRACTION99.974
2.682-2.770.2811600.2343629X-RAY DIFFRACTION100
2.77-2.8670.2911860.2443436X-RAY DIFFRACTION99.9724
2.867-2.9750.311980.2473316X-RAY DIFFRACTION99.9715
2.975-3.0960.2871770.2563228X-RAY DIFFRACTION99.9706
3.096-3.2330.3131520.2473110X-RAY DIFFRACTION99.9694
3.233-3.390.2541610.2492924X-RAY DIFFRACTION99.9676
3.39-3.5730.2861440.2522845X-RAY DIFFRACTION99.9666
3.573-3.7880.2651480.2422662X-RAY DIFFRACTION100
3.788-4.0480.2761510.2422530X-RAY DIFFRACTION100
4.048-4.370.231300.2262362X-RAY DIFFRACTION100
4.37-4.7830.2191310.232154X-RAY DIFFRACTION100
4.783-5.3420.2461290.2531964X-RAY DIFFRACTION100
5.342-6.1570.285840.311775X-RAY DIFFRACTION100
6.157-7.5120.327850.3181510X-RAY DIFFRACTION100
7.512-10.5060.255710.2461199X-RAY DIFFRACTION99.9213
10.506-49.7930.355320.331711X-RAY DIFFRACTION95.7474

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