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- PDB-5xwz: Crystal structure of a lactonase from Cladophialophora bantiana -

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Basic information

Entry
Database: PDB / ID: 5xwz
TitleCrystal structure of a lactonase from Cladophialophora bantiana
ComponentsUnplaced genomic scaffold supercont1.36, whole genome shotgun sequence
KeywordsHYDROLASE / ALPHA/BETA-HYDROLASE / LACTONASE / ZEARALENONE
Function / homology
Function and homology information


glycerolipid catabolic process / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / triacylglycerol lipase activity / response to toxic substance
Similarity search - Function
: / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
MALONATE ION / Zearalenone hydrolase
Similarity search - Component
Biological speciesCladophialophora bantiana CBS 173.52 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsZheng, Y.Y. / Liu, W.T. / Liu, W.D. / Chen, C.C. / Guo, R.T.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2017
Title: Characterization and crystal structure of a novel zearalenone hydrolase from Cladophialophora bantiana
Authors: Hui, R. / Hu, X. / Liu, W. / Liu, W. / Zheng, Y. / Chen, Y. / Guo, R.T. / Jin, J. / Chen, C.C.
History
DepositionJun 30, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Unplaced genomic scaffold supercont1.36, whole genome shotgun sequence
B: Unplaced genomic scaffold supercont1.36, whole genome shotgun sequence
C: Unplaced genomic scaffold supercont1.36, whole genome shotgun sequence
D: Unplaced genomic scaffold supercont1.36, whole genome shotgun sequence
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,30713
Polymers119,7354
Non-polymers5729
Water19,1141061
1
A: Unplaced genomic scaffold supercont1.36, whole genome shotgun sequence
B: Unplaced genomic scaffold supercont1.36, whole genome shotgun sequence
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2007
Polymers59,8672
Non-polymers3325
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-30 kcal/mol
Surface area20490 Å2
MethodPISA
2
C: Unplaced genomic scaffold supercont1.36, whole genome shotgun sequence
D: Unplaced genomic scaffold supercont1.36, whole genome shotgun sequence
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1076
Polymers59,8672
Non-polymers2404
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-25 kcal/mol
Surface area20140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.863, 104.399, 116.834
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-458-

HOH

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Components

#1: Protein
Unplaced genomic scaffold supercont1.36, whole genome shotgun sequence


Mass: 29933.666 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cladophialophora bantiana CBS 173.52 (fungus)
Gene: Z519_12792 / Plasmid: pET-46 EK/LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0D2H023
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1061 / 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: 3.08 Å3/Da / Density % sol: 60.04 % / Mosaicity: 0.456 °
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 1.4M Sodium Malonate, 0.1M Bis-Tris Propane pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 29, 2016
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→25 Å / Num. obs: 148988 / % possible obs: 99.9 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.026 / Rrim(I) all: 0.055 / Χ2: 1.36 / Net I/σ(I): 13.4 / Num. measured all: 621889
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.75-1.814.10.480.8280.2710.5521.27199.9
1.81-1.894.10.3450.9060.1940.3971.30499.9
1.89-1.974.20.2290.9560.1280.2631.31499.9
1.97-2.074.20.1650.9760.0920.1891.33499.9
2.07-2.24.20.1260.9860.070.1451.49899.9
2.2-2.374.20.0920.9920.0520.1061.64399.8
2.37-2.614.20.0670.9950.0370.0771.37199.9
2.61-2.994.20.0490.9960.0270.0561.39899.8
2.99-3.774.10.0350.9980.020.041.66699.9
3.77-254.20.0210.9990.0110.0240.83499.9

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WZL

3wzl


Resolution: 1.75→25 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.811 / SU ML: 0.057 / SU R Cruickshank DPI: 0.0783 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.078 / ESU R Free: 0.082
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1806 7478 5 %RANDOM
Rwork0.1545 ---
obs0.1558 141307 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 147.51 Å2 / Biso mean: 27.676 Å2 / Biso min: 13.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å2-
2--0.78 Å2-0 Å2
3----0.91 Å2
Refinement stepCycle: final / Resolution: 1.75→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8096 0 36 1061 9193
Biso mean--49.77 37.13 -
Num. residues----1048
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0198356
X-RAY DIFFRACTIONr_bond_other_d0.0010.027526
X-RAY DIFFRACTIONr_angle_refined_deg1.4851.95611392
X-RAY DIFFRACTIONr_angle_other_deg0.851317509
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.06851046
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.17323.778360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.419151292
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5141552
X-RAY DIFFRACTIONr_chiral_restr0.1320.21249
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0219363
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021681
LS refinement shellResolution: 1.75→1.795 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 533 -
Rwork0.237 10303 -
all-10836 -
obs--99.85 %

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