[English] 日本語
Yorodumi
- PDB-5z7j: Crystal structure of a lactonase double mutant in complex with li... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5z7j
TitleCrystal structure of a lactonase double mutant in complex with ligand l
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-36J / DI(HYDROXYETHYL)ETHER / AB hydrolase-1 domain-containing protein
Function and homology information
Biological speciesRhinocladiella mackenziei CBS 650.93 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 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
DepositionJan 29, 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
E: Lactonase for protein
F: Lactonase for protein
G: Lactonase for protein
H: Lactonase for protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)236,01418
Polymers233,2398
Non-polymers2,77510
Water33,5801864
1
A: Lactonase for protein
C: Lactonase for protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9504
Polymers58,3102
Non-polymers6412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-10 kcal/mol
Surface area20000 Å2
MethodPISA
2
B: Lactonase for protein
D: Lactonase for protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1636
Polymers58,3102
Non-polymers8534
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-10 kcal/mol
Surface area20170 Å2
MethodPISA
3
E: Lactonase for protein
H: Lactonase for protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9504
Polymers58,3102
Non-polymers6412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-12 kcal/mol
Surface area19700 Å2
MethodPISA
4
F: Lactonase for protein
G: Lactonase for protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9504
Polymers58,3102
Non-polymers6412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-11 kcal/mol
Surface area19980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.335, 94.759, 100.449
Angle α, β, γ (deg.)90.730, 92.360, 91.590
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Lactonase for protein


Mass: 29154.854 Da / Num. of mol.: 8 / Fragment: UNP residues 3-266
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhinocladiella mackenziei CBS 650.93 (fungus)
Gene: Z518_04590 / Plasmid: pET-46 EK/LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0D2ILK1
#2: Chemical
ChemComp-36J / (3S,7R,11E)-7,14,16-trihydroxy-3-methyl-3,4,5,6,7,8,9,10-octahydro-1H-2-benzoxacyclotetradecin-1-one


Mass: 320.380 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C18H24O5
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1864 / 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: 3.07 Å3/Da / Density % sol: 59.94 % / Mosaicity: 0.908 °
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 and 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: 1.98→25 Å / Num. obs: 188099 / % possible obs: 97.7 % / Redundancy: 4 % / Biso Wilson estimate: 30.94 Å2 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.042 / Rrim(I) all: 0.085 / Χ2: 0.705 / Net I/σ(I): 10.6 / Num. measured all: 752400
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.98-2.053.90.66185760.8710.3830.7641.05296.5
2.05-2.133.90.486186290.8430.2820.5621.06296.7
2.13-2.2340.366186740.8670.2120.4231.00597
2.23-2.3540.25187340.9550.1440.2890.89697.3
2.35-2.4940.195187890.9690.1120.2250.80397.5
2.49-2.6940.141188490.9770.0810.1630.7397.7
2.69-2.9640.095188670.990.0550.110.57498.1
2.96-3.3840.063189460.9950.0360.0730.43298.4
3.38-4.2640.043189790.9970.0250.050.28198.6
4.26-2540.039190560.9970.0230.0460.25998.9

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX(1.12_2829: ???)refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IE4

5ie4


Resolution: 1.98→24.714 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 22.46
RfactorNum. reflection% reflection
Rfree0.2095 2002 1.06 %
Rwork0.1659 --
obs0.1663 188061 97.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 90.35 Å2 / Biso mean: 36.0956 Å2 / Biso min: 18.93 Å2
Refinement stepCycle: final / Resolution: 1.98→24.714 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16384 0 198 1864 18446
Biso mean--43.88 41.75 -
Num. residues----2106
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00817049
X-RAY DIFFRACTIONf_angle_d0.95323281
X-RAY DIFFRACTIONf_chiral_restr0.0572538
X-RAY DIFFRACTIONf_plane_restr0.0073032
X-RAY DIFFRACTIONf_dihedral_angle_d12.83410120
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9797-2.05040.28682030.2442178161801993
2.0504-2.13240.29911990.2269184451864497
2.1324-2.22940.27781820.2114185291871197
2.2294-2.34690.2672050.1927186331883897
2.3469-2.49380.2252080.1846186261883497
2.4938-2.68610.23941950.1811186871888298
2.6861-2.9560.23742070.1757187421894998
2.956-3.38280.19452010.1659188261902798
3.3828-4.25850.18592000.1425188361903699
4.2585-24.71630.16632020.1389189191912199

+
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