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- PDB-8jlv: Beneficial flip of substrate orientation enable determine substra... -

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Basic information

Entry
Database: PDB / ID: 8jlv
TitleBeneficial flip of substrate orientation enable determine substrate specificity for zearalenone lactone hydrolase
ComponentsAB hydrolase-1 domain-containing protein
KeywordsHYDROLASE / mycotoxin / zearalenone hydrolase
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 speciesExophiala aquamarina CBS 119918 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99863596858 Å
AuthorsXiang, L. / Wang, M. / Zhang, G. / Zhou, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31970059 China
CitationJournal: Appl.Environ.Microbiol. / Year: 2024
Title: Enhancing the activity of zearalenone lactone hydrolase toward the more toxic alpha-zearalanol via a single-point mutation.
Authors: Wang, M. / Zhang, F. / Xiang, L. / Li, M. / Lu, Z. / Wu, P. / Sheng, X. / Zhou, J. / Zhang, G.
History
DepositionJun 2, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: AB hydrolase-1 domain-containing protein
A: AB hydrolase-1 domain-containing protein
C: AB hydrolase-1 domain-containing protein
D: AB hydrolase-1 domain-containing protein
E: AB hydrolase-1 domain-containing protein
F: AB hydrolase-1 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)175,8856
Polymers175,8856
Non-polymers00
Water00
1
B: AB hydrolase-1 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)29,3141
Polymers29,3141
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: AB hydrolase-1 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)29,3141
Polymers29,3141
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: AB hydrolase-1 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)29,3141
Polymers29,3141
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: AB hydrolase-1 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)29,3141
Polymers29,3141
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: AB hydrolase-1 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)29,3141
Polymers29,3141
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: AB hydrolase-1 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)29,3141
Polymers29,3141
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.892, 120.326, 102.952
Angle α, β, γ (deg.)90.000, 97.415, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 1 - 264 / Label seq-ID: 1 - 264

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain 'A'AB
2chain 'B'BA
3chain 'C'CC
4chain 'D'DD
5chain 'E'EE
6chain 'F'FF

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Components

#1: Protein
AB hydrolase-1 domain-containing protein / ZEN lactone hydrolase / ZHDAY3


Mass: 29314.209 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Exophiala aquamarina CBS 119918 (fungus)
Gene: A1O9_11392 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A072PAD1

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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: 2.79 Å3/Da / Density % sol: 55.91 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 1M NaH2PO4/K2HPO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.99→50 Å / Num. obs: 38647 / % possible obs: 96.7 % / Redundancy: 6.7 % / Biso Wilson estimate: 60.5318838754 Å2 / Rmerge(I) obs: 0.319 / Net I/σ(I): 8
Reflection shellResolution: 3→3.05 Å / Rmerge(I) obs: 1.457 / Num. unique obs: 38647

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PHENIX1.11.1_2575refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.99863596858→42.7041738183 Å / SU ML: 0.404588603442 / Cross valid method: FREE R-VALUE / σ(F): 1.35996978708 / Phase error: 25.8442308199
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.246848482999 1830 4.87739872068 %
Rwork0.20354976524 35690 -
obs0.205645544032 37520 96.6711326394 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.4335054379 Å2
Refinement stepCycle: LAST / Resolution: 2.99863596858→42.7041738183 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12360 0 0 0 12360
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093848086519712702
X-RAY DIFFRACTIONf_angle_d1.3714321779517334
X-RAY DIFFRACTIONf_chiral_restr0.07351513783471914
X-RAY DIFFRACTIONf_plane_restr0.008066090976522232
X-RAY DIFFRACTIONf_dihedral_angle_d13.26055611957560
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.07970.3605707045181000.3149375452062053X-RAY DIFFRACTION72.3940820444
3.0797-3.17030.3964297196541320.3060068400352510X-RAY DIFFRACTION89.1062394604
3.1703-3.27260.2943451405211430.2848034872052726X-RAY DIFFRACTION97.089678511
3.2726-3.38950.3100213122791360.2576438119672808X-RAY DIFFRACTION99.3923024983
3.3895-3.52510.323861941781420.2512760469392843X-RAY DIFFRACTION99.7327096559
3.5251-3.68550.2585268752261650.2283233687792805X-RAY DIFFRACTION99.932705249
3.6855-3.87970.2375309501641530.2028121332332806X-RAY DIFFRACTION99.9662162162
3.8797-4.12260.2274101900381630.1840699892062820X-RAY DIFFRACTION100
4.1226-4.44060.2104461184971400.1657463094442866X-RAY DIFFRACTION100
4.4406-4.88690.1997719389771420.1605041032012836X-RAY DIFFRACTION100
4.8869-5.59270.2127185750791310.174498319162860X-RAY DIFFRACTION100
5.5927-7.04110.2345793183661350.1985643674212865X-RAY DIFFRACTION99.8668442077
7.0411-8.130.2245053608091480.1801507887352892X-RAY DIFFRACTION99.1519895629

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