[English] 日本語
Yorodumi
- PDB-5c81: ZHD-Intermediate complex after ZHD crystal soaking in ZEN for 12min -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5c81
TitleZHD-Intermediate complex after ZHD crystal soaking in ZEN for 12min
ComponentsZearalenone hydrolase
KeywordsHYDROLASE / lactonase / alpha-beta fold / zearalenone degrade intermediate
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / response to toxic substance / hydrolase activity
Similarity search - Function
: / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / : / Chem-ZFR / Zearalenone hydrolase
Similarity search - Component
Biological speciesClonostachys rosea (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHu, X.-J. / Qi, Q. / Yang, W.-J.
Funding support China, 3items
OrganizationGrant numberCountry
Chinese High-tech Research and Development program2013AA102803B China
Chinese High-tech Research and Development program2014AA021301 China
973 Program of the Ministry of Science and Technology of China2009CB918602 China
CitationJournal: To Be Published
Title: A Case Study of Lactonase ZHD
Authors: Ming, D.-M. / Qi, Q. / Yang, W.-J. / Sun, K.-L. / Xu, T.-Y. / Huang, Q. / Hu, X.-J. / Lv, H.
History
DepositionJun 25, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Zearalenone hydrolase
B: Zearalenone hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8398
Polymers62,0382
Non-polymers8016
Water8,989499
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-17 kcal/mol
Surface area20540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.530, 90.080, 112.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Zearalenone hydrolase


Mass: 31018.973 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clonostachys rosea (fungus) / Gene: zhd101 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NKB0

-
Non-polymers , 5 types, 505 molecules

#2: Chemical ChemComp-ZFR / (1E,10S)-1-(3,5-dihydroxyphenyl)-10-hydroxyundec-1-en-6-one


Mass: 292.370 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H24O4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 499 / Source method: isolated from a natural source / Formula: H2O

-
Details

Nonpolymer detailsZFR and FMT are used to simulate the intermediate in the crystal structure.
Sequence detailsThe strain of Clonostachys rosea is different from UNP Q8NKB0.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.29 Å3/Da / Density % sol: 62.58 %
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

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97923 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 70972 / % possible obs: 99.8 % / Redundancy: 13.7 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 22.4
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.536 / Mean I/σ(I) obs: 6.7 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WZL

3wzl


Resolution: 1.8→47.84 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1755 3471 4.9 %Random selection
Rwork0.1479 ---
obs0.1493 70897 99.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→47.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4094 0 53 499 4646
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074448
X-RAY DIFFRACTIONf_angle_d1.0586107
X-RAY DIFFRACTIONf_dihedral_angle_d11.9451613
X-RAY DIFFRACTIONf_chiral_restr0.045688
X-RAY DIFFRACTIONf_plane_restr0.005801
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8001-1.82470.1961480.17952647X-RAY DIFFRACTION100
1.8247-1.85080.17071300.15912673X-RAY DIFFRACTION100
1.8508-1.87840.16821410.14822652X-RAY DIFFRACTION100
1.8784-1.90780.17471300.14272668X-RAY DIFFRACTION100
1.9078-1.9390.19281370.14352641X-RAY DIFFRACTION100
1.939-1.97250.24191400.1432672X-RAY DIFFRACTION100
1.9725-2.00840.19351310.14412708X-RAY DIFFRACTION100
2.0084-2.0470.17561460.15022652X-RAY DIFFRACTION100
2.047-2.08880.18331380.14532663X-RAY DIFFRACTION100
2.0888-2.13420.1691390.14532673X-RAY DIFFRACTION100
2.1342-2.18380.15961280.13892675X-RAY DIFFRACTION100
2.1838-2.23840.16111370.13912676X-RAY DIFFRACTION100
2.2384-2.2990.17251540.14292679X-RAY DIFFRACTION100
2.299-2.36660.1871500.14892658X-RAY DIFFRACTION100
2.3666-2.4430.17691460.14762689X-RAY DIFFRACTION100
2.443-2.53030.18851290.14722691X-RAY DIFFRACTION100
2.5303-2.63160.19881470.15192689X-RAY DIFFRACTION100
2.6316-2.75140.19771240.15132709X-RAY DIFFRACTION100
2.7514-2.89640.18061470.15262695X-RAY DIFFRACTION100
2.8964-3.07780.1811470.15872706X-RAY DIFFRACTION100
3.0778-3.31540.16361230.15082737X-RAY DIFFRACTION100
3.3154-3.6490.14631320.14722720X-RAY DIFFRACTION100
3.649-4.17670.15441290.13192772X-RAY DIFFRACTION100
4.1767-5.26120.16011300.13722784X-RAY DIFFRACTION100
5.2612-47.85660.19161680.17092897X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 18.3287 Å / Origin y: 16.3747 Å / Origin z: -5.7321 Å
111213212223313233
T0.0833 Å20.0035 Å2-0.006 Å2-0.1158 Å2-0.0231 Å2--0.12 Å2
L0.2325 °2-0.0069 °2-0.0336 °2-0.6786 °2-0.5041 °2--0.7948 °2
S0.0112 Å °0.0124 Å °-0.0037 Å °-0.0252 Å °0.008 Å °0.0339 Å °0.0139 Å °0.0359 Å °-0.0172 Å °
Refinement TLS groupSelection details: ALL

+
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