[English] 日本語
Yorodumi
- PDB-5z97: Crystal structure of a lactonase double mutant in complex with li... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5z97
TitleCrystal structure of a lactonase double mutant in complex with ligand N
ComponentsLactonase for protein
KeywordsHYDROLASE / ALPHA/BETA-HYDROLASE / LACTONASE / ZEARALENONE
Function / homology: / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / Chem-ZER / AB hydrolase-1 domain-containing protein
Function and homology information
Biological speciesRhinocladiella mackenziei CBS 650.93 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsZheng, Y.Y. / Liu, W.D. / Chen, C.C. / Guo, R.T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31400678, 31470240, 31500642, 31570130, 31600058, and 31600638 China
CitationJournal: Acs Catalysis / Year: 2018
Title: Crystal Structure of a Mycoestrogen-Detoxifying Lactonase from Rhinocladiella mackenziei: Molecular Insight into ZHD Substrate Selectivity
Authors: Zheng, Y.Y. / Liu, W.T. / Chen, C.C. / Hu, X.Y. / Liu, W.D. / Ko, T.P. / Tang, X.K. / Wei, H.L. / Huang, J.W. / Guo, R.T.
History
DepositionFeb 2, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lactonase for protein
B: Lactonase for protein
C: Lactonase for protein
D: Lactonase for protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,3868
Polymers116,3354
Non-polymers1,0514
Water4,504250
1
A: Lactonase for protein
B: Lactonase for protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9005
Polymers58,1682
Non-polymers7333
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-24 kcal/mol
Surface area19710 Å2
MethodPISA
2
C: Lactonase for protein
D: Lactonase for protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4863
Polymers58,1682
Non-polymers3181
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-11 kcal/mol
Surface area20310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.319, 110.520, 127.779
Angle α, β, γ (deg.)90.00, 99.93, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Lactonase for protein


Mass: 29083.775 Da / Num. of mol.: 4 / Fragment: UNP residues 4-266
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhinocladiella mackenziei CBS 650.93 (fungus)
Plasmid: pET-46 EK/LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0D2ILK1
#2: Chemical ChemComp-ZER / (3S,11E)-14,16-dihydroxy-3-methyl-3,4,5,6,9,10-hexahydro-1H-2-benzoxacyclotetradecine-1,7(8H)-dione / Zearalenone


Mass: 318.364 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H22O5
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.58 % / Mosaicity: 0.656 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Ammonium Sulfate, 0.085M Sodium Cacodylate pH 6.5, 25-28%(w/v) Polyethylene Glycol 8000, 15%(v/v) Glycerol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Aug 2, 2017
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.32→25 Å / Num. obs: 50048 / % possible obs: 95 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.038 / Rrim(I) all: 0.077 / Χ2: 1.083 / Net I/σ(I): 12.6 / Num. measured all: 194860
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.32-2.43.80.48650580.8030.2760.5611.21496.6
2.4-2.53.80.42649740.8510.240.4911.17594.8
2.5-2.613.80.32549880.8860.1840.3751.15794.2
2.61-2.753.80.23349700.9390.1320.2691.05595
2.75-2.923.90.17148790.9620.0970.1981.01293.5
2.92-3.153.90.1148590.9830.0630.1281.0592
3.15-3.463.90.08748580.9850.050.11.01392.1
3.46-3.963.90.06248860.9920.0350.0721.00793.3
3.96-4.993.90.03852210.9970.0220.0441.10298.4
4.99-254.20.03153550.9980.0170.0361.05299.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IE4

5ie4


Resolution: 2.32→25 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.897 / SU B: 9.166 / SU ML: 0.217 / Cross valid method: THROUGHOUT / ESU R: 0.398 / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26634 2490 5 %RANDOM
Rwork0.20958 ---
obs0.21236 47531 94.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.23 Å2
Baniso -1Baniso -2Baniso -3
1--1.8 Å2-0 Å20.53 Å2
2--0.12 Å2-0 Å2
3---1.41 Å2
Refinement stepCycle: 1 / Resolution: 2.32→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8174 0 74 250 8498
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0198482
X-RAY DIFFRACTIONr_bond_other_d0.0010.027660
X-RAY DIFFRACTIONr_angle_refined_deg1.1961.96811586
X-RAY DIFFRACTIONr_angle_other_deg0.7253.00317825
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.81551046
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.46923.626364
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.143151298
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0721552
X-RAY DIFFRACTIONr_chiral_restr0.0770.21261
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0219456
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021694
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_it5.2544.8224196
X-RAY DIFFRACTIONr_mcbond_other5.2514.8214195
X-RAY DIFFRACTIONr_mcangle_it7.257.2145238
X-RAY DIFFRACTIONr_mcangle_other7.257.2165239
X-RAY DIFFRACTIONr_scbond_it5.224.994286
X-RAY DIFFRACTIONr_scbond_other5.2194.9914287
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.0867.3956349
X-RAY DIFFRACTIONr_long_range_B_refined10.61690.42539546
X-RAY DIFFRACTIONr_long_range_B_other10.61590.42139545
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.317→2.377 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 208 -
Rwork0.292 3483 -
obs--95.8 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more