[English] 日本語
Yorodumi
- PDB-9xv5: Catalytic domain of N1484 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9xv5
TitleCatalytic domain of N1484
ComponentsLipase
KeywordsHYDROLASE / PET hydrolase
Function / homology
Function and homology information


carboxylic ester hydrolase activity
Similarity search - Function
Cutinase / PET hydrolase-like / : / Ricin-type beta-trefoil lectin domain / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Biological speciesMicromonospora ureilytica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsHwang, H. / Seo, H. / Kim, K.-J.
Funding support Korea, Republic Of, 4items
OrganizationGrant numberCountry
Other governmentRS-2025-10702985
Other governmentRS-2025-06082970
National Research Foundation (NRF, Korea)RS-2024-00439872 Korea, Republic Of
Other governmentP0028353
CitationJournal: J Hazard Mater / Year: 2026
Title: Effect of surface electrostatic potential on pH-activity profile in PET depolymerases.
Authors: Seo, H. / Hwang, H. / Park, J. / Ki, D. / Choi, W. / Yoon, Y. / Kim, D. / Kim, K.J.
History
DepositionNov 25, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 3, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7573
Polymers28,6031
Non-polymers1542
Water5,044280
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-0 kcal/mol
Surface area9620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.239, 84.212, 43.853
Angle α, β, γ (deg.)90.00, 92.78, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Lipase / C3 cluster PET hydrolase


Mass: 28603.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora ureilytica (bacteria) / Gene: DDE19_30945 / Production host: Escherichia coli (E. coli) / Variant (production host): SHuffle T7 / References: UniProt: A0A3N9XER1
#2: 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
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 30% (v/v) PEG 8000, 0.1M imidazole (pH 8.0), 0.2M sodium chloride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 29, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.4→43.8 Å / Num. obs: 48448 / % possible obs: 98.7 % / Redundancy: 3.7 % / CC1/2: 0.99 / Rmerge(I) obs: 0.077 / Net I/σ(I): 12.2
Reflection shellResolution: 1.4→1.448 Å / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4862 / CC1/2: 0.754

-
Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→43.8 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.039 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17684 2473 5.1 %RANDOM
Rwork0.15278 ---
obs0.15398 45975 98.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.746 Å2
Baniso -1Baniso -2Baniso -3
1-0.97 Å2-0 Å20.03 Å2
2---0.83 Å2-0 Å2
3----0.14 Å2
Refinement stepCycle: 1 / Resolution: 1.4→43.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1922 0 10 280 2212
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0112093
X-RAY DIFFRACTIONr_bond_other_d0.0020.0161927
X-RAY DIFFRACTIONr_angle_refined_deg1.831.6482873
X-RAY DIFFRACTIONr_angle_other_deg0.6221.5564434
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2495281
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.451516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.80310296
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.10.2327
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022555
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02501
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_it1.2770.9791094
X-RAY DIFFRACTIONr_mcbond_other1.2780.9761093
X-RAY DIFFRACTIONr_mcangle_it1.8441.7561385
X-RAY DIFFRACTIONr_mcangle_other1.8451.7581386
X-RAY DIFFRACTIONr_scbond_it1.9871.187999
X-RAY DIFFRACTIONr_scbond_other1.9871.1871000
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9192.0771489
X-RAY DIFFRACTIONr_long_range_B_refined8.90823.072506
X-RAY DIFFRACTIONr_long_range_B_other8.35117.442392
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.434 Å
RfactorNum. reflection% reflection
Rfree0.272 174 -
Rwork0.245 3423 -
obs--99.04 %

+
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