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- PDB-5xmw: Selenomethionine-derivated ZHD -

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Basic information

Entry
Database: PDB / ID: 5xmw
TitleSelenomethionine-derivated ZHD
ComponentsZearalenone lactonase
KeywordsHYDROLASE / LACTONASE / ALPHA-BETA FOLD / ZEARALENONE DEGRADE
Function / homology: / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / response to toxic substance / Alpha/Beta hydrolase fold / hydrolase activity / Zearalenone lactonase / Zearalenone hydrolase
Function and homology information
Biological speciesBionectria ochroleuca (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsHu, X.J.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2017
Title: The structure of a complex of the lactonohydrolase zearalenone hydrolase with the hydrolysis product of zearalenone at 1.60 angstrom resolution
Authors: Qi, Q. / Yang, W.J. / Zhou, H.J. / Ming, D.M. / Sun, K.L. / Xu, T.Y. / Hu, X.J. / Lv, H.
History
DepositionMay 16, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Zearalenone lactonase
B: Zearalenone lactonase


Theoretical massNumber of molelcules
Total (without water)62,6942
Polymers62,6942
Non-polymers00
Water905
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, dimeric
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-13 kcal/mol
Surface area21560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.924, 90.169, 113.056
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MSE / Beg label comp-ID: MSE / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 1 - 267 / Label seq-ID: 1 - 267

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Zearalenone lactonase


Mass: 31347.234 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bionectria ochroleuca (fungus) / Gene: ZHD101 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0N9XBU7, UniProt: Q8NKB0*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE STRAIN OF CLONOSTACHYS ROSEA IS DIFFERENT FROM UNP A0A0N9XBU7.

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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: 3.01 Å3/Da / Density % sol: 59.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 1.2 M AMMONIUM DIBASIC PHOSPHATE, 200 MM KCL, 100 MM IMIDAZOLE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97869 Å
DetectorType: ADSC QUANTUM 315r / Detector: AREA DETECTOR / Date: Sep 7, 2014
RadiationMonochromator: 0.99 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97869 Å / Relative weight: 1
ReflectionResolution: 3→50.01 Å / Num. obs: 14839 / % possible obs: 99.6 % / Redundancy: 13.6 % / Biso Wilson estimate: 73.9 Å2 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.038 / Net I/σ(I): 9.31
Reflection shellResolution: 3→3.076 Å / Redundancy: 14.5 % / Rmerge(I) obs: 0.512 / Num. unique obs: 1072 / Rpim(I) all: 0.139 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000v1.0data reduction
HKL-2000v1.0data scaling
PHENIXv 1.9phasing
RefinementMethod to determine structure: SAD / Resolution: 3→50.01 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.923 / SU B: 15.38 / SU ML: 0.277 / Cross valid method: THROUGHOUT / ESU R Free: 0.381 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23585 805 5.1 %RANDOM
Rwork0.20767 ---
obs0.20913 14839 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 75.03 Å2
Baniso -1Baniso -2Baniso -3
1--7.97 Å2-0 Å20 Å2
2--7.57 Å2-0 Å2
3---0.39 Å2
Refinement stepCycle: 1 / Resolution: 3→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4117 0 0 5 4122
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194245
X-RAY DIFFRACTIONr_bond_other_d0.0020.023851
X-RAY DIFFRACTIONr_angle_refined_deg1.3431.9565808
X-RAY DIFFRACTIONr_angle_other_deg0.9238946
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4085540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.01424.138174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.22615615
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2151520
X-RAY DIFFRACTIONr_chiral_restr0.0740.2665
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214752
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02836
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.0377.4692160
X-RAY DIFFRACTIONr_mcbond_other6.0377.4672159
X-RAY DIFFRACTIONr_mcangle_it8.51611.2282700
X-RAY DIFFRACTIONr_mcangle_other8.51411.2312701
X-RAY DIFFRACTIONr_scbond_it6.8567.8422085
X-RAY DIFFRACTIONr_scbond_other6.8567.8422085
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.57311.5763109
X-RAY DIFFRACTIONr_long_range_B_refined13.15617507
X-RAY DIFFRACTIONr_long_range_B_other13.15517508
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 17046 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.998→3.076 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.442 52 -
Rwork0.301 1072 -
obs--98.34 %

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