[English] 日本語
Yorodumi
- PDB-8z4s: The crystal structure of a Hydroquinone Dioxygenase PaD with nonn... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8z4s
TitleThe crystal structure of a Hydroquinone Dioxygenase PaD with nonnatural substrate S6
ComponentsHydroquinone Dioxygenase PaD
KeywordsOXIDOREDUCTASE / Hydroquinone Dioxygenase
Function / homology: / ACETATE ION / : / FORMIC ACID / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesAspergillus westerdijkiae (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsLiu, Z.W. / Huang, J.-W. / Wang, Y.X. / Chen, C.-C. / Guo, R.-T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2024
Title: Substrate specificity of a branch of aromatic dioxygenases determined by three distinct motifs.
Authors: Cui, C. / Yang, L.J. / Liu, Z.W. / Shu, X. / Zhang, W.W. / Gao, Y. / Wang, Y.X. / Wang, T. / Chen, C.C. / Guo, R.T. / Gao, S.S.
History
DepositionApr 17, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hydroquinone Dioxygenase PaD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8609
Polymers54,1971
Non-polymers6638
Water6,395355
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.831, 119.831, 92.889
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Hydroquinone Dioxygenase PaD


Mass: 54196.941 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus westerdijkiae (mold) / Production host: Escherichia coli BL21(DE3) (bacteria)

-
Non-polymers , 7 types, 363 molecules

#2: Chemical ChemComp-A1D7Z / 2,3,5-trimethylbenzene-1,4-diol / Trimethylhydroquinone


Mass: 152.190 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.56 Å3/Da / Density % sol: 65.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 0.1 M HEPES 7.0; 24% PEG Smear Medium; 7% Tacsimate 7.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.9998 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Nov 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 1.93→25 Å / Num. obs: 56510 / % possible obs: 99.7 % / Redundancy: 6 % / CC1/2: 0.997 / Net I/σ(I): 31.6
Reflection shellResolution: 1.93→2 Å / Num. unique obs: 5604 / CC1/2: 0.934

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
SAINTdata scaling
SAINTdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→24.48 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.12 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24973 2865 5.1 %RANDOM
Rwork0.20905 ---
obs0.21116 53273 98.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å2-0.19 Å2-0 Å2
2---0.38 Å20 Å2
3---1.24 Å2
Refinement stepCycle: 1 / Resolution: 1.93→24.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3743 0 42 357 4142
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0133872
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173466
X-RAY DIFFRACTIONr_angle_refined_deg1.6581.6495232
X-RAY DIFFRACTIONr_angle_other_deg1.4261.5798015
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3585462
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.14421.152243
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.82215631
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4841536
X-RAY DIFFRACTIONr_chiral_restr0.0910.2481
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024397
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02887
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_it3.6323.6621852
X-RAY DIFFRACTIONr_mcbond_other3.6333.6641853
X-RAY DIFFRACTIONr_mcangle_it4.2675.4662312
X-RAY DIFFRACTIONr_mcangle_other4.2665.4682313
X-RAY DIFFRACTIONr_scbond_it3.8124.0292019
X-RAY DIFFRACTIONr_scbond_other3.8114.032020
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2075.9052921
X-RAY DIFFRACTIONr_long_range_B_refined6.36943.9394577
X-RAY DIFFRACTIONr_long_range_B_other6.33643.6184511
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.932→1.982 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 239 -
Rwork0.32 3817 -
obs--97.76 %

+
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