[English] 日本語
Yorodumi
- PDB-9lmv: Crystal structure of FAST-ACC-T140D/R132G/S160A mutant in complex... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9lmv
TitleCrystal structure of FAST-ACC-T140D/R132G/S160A mutant in complex with mono(2-hydroxyethyl) terephthalic acid
ComponentsPoly(ethylene terephthalate) hydrolase
KeywordsHYDROLASE / PET hydrolase / PET degradation enzyme
Function / homology
Function and homology information


acetylesterase activity / poly(ethylene terephthalate) hydrolase / carboxylic ester hydrolase activity / xenobiotic catabolic process / extracellular region
Similarity search - Function
Cutinase / PET hydrolase-like / : / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
4-(2-hydroxyethyloxycarbonyl)benzoic acid / Poly(ethylene terephthalate) hydrolase
Similarity search - Component
Biological speciesPiscinibacter sakaiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsLi, X. / Ning, Z.Y. / Huang, S.Q. / Zeng, C. / Zeng, Z.Y. / Ji, R. / Huang, J.-W. / Chen, C.-C. / Guo, R.-T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Int.J.Biol.Macromol. / Year: 2025
Title: Combined approaches to enhance the Pichia pastoris-expressed PET hydrolase.
Authors: Li, X. / Huang, J.W. / Ning, Z. / Huang, S. / Zeng, C. / Zeng, Z. / Ji, R. / Peng, R. / Liu, X. / Min, J. / Chen, C.C. / Guo, R.T.
History
DepositionJan 20, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Poly(ethylene terephthalate) hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4992
Polymers27,2891
Non-polymers2101
Water5,260292
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.852, 50.961, 83.969
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Poly(ethylene terephthalate) hydrolase / PET hydrolase / PETase / PET-digesting enzyme


Mass: 27289.312 Da / Num. of mol.: 1 / Mutation: R132G,T140D,S160A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Piscinibacter sakaiensis (bacteria) / Gene: ISF6_4831 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0K8P6T7, poly(ethylene terephthalate) hydrolase
#2: Chemical ChemComp-C9C / 4-(2-hydroxyethyloxycarbonyl)benzoic acid / monohydroxyethyl terephthalate


Mass: 210.183 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H10O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.3 M (NH4)2SO4, 0.2 M NaCl, 0.1 M Bis-Tris, pH 6.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 07A / Wavelength: 0.97621 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 24, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97621 Å / Relative weight: 1
ReflectionResolution: 1.57→25 Å / Num. obs: 29953 / % possible obs: 95.9 % / Redundancy: 5.2 % / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.022 / Rrim(I) all: 0.052 / Χ2: 1.243 / Net I/σ(I): 29.2 / Num. measured all: 155392
Reflection shell

CC star: 0.999 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.57-1.635.40.05129490.9970.0240.0561.39195.7
1.63-1.695.20.0529430.9960.0240.0561.2196
1.69-1.775.20.04929590.9950.0240.0551.19796.6
1.77-1.865.10.04729760.9960.0230.0531.2296.5
1.86-1.984.90.04729410.9960.0230.0521.25495.2
1.98-2.135.30.04530210.9960.0220.051.31696.8
2.13-2.345.30.04430300.9970.0210.0491.29397.7
2.34-2.685.20.04430440.9960.0210.0491.32796.9
2.68-3.385.20.04530570.9960.0210.051.06796.1
3.38-2550.04830330.9960.0230.0541.14391.3

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.57→24.54 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.986 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14962 1424 4.8 %RANDOM
Rwork0.09765 ---
obs0.10011 28498 95.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.078 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å2-0 Å20 Å2
2--0.39 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.57→24.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1913 0 15 292 2220
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0131989
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171731
X-RAY DIFFRACTIONr_angle_refined_deg2.4011.6472717
X-RAY DIFFRACTIONr_angle_other_deg1.8461.5724038
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.695268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.82622.35385
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.85915281
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2671510
X-RAY DIFFRACTIONr_chiral_restr0.1760.2270
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.022311
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02415
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_it1.6840.6641057
X-RAY DIFFRACTIONr_mcbond_other1.6840.6631056
X-RAY DIFFRACTIONr_mcangle_it1.7960.9951321
X-RAY DIFFRACTIONr_mcangle_other1.7960.9961322
X-RAY DIFFRACTIONr_scbond_it2.0030.827932
X-RAY DIFFRACTIONr_scbond_other2.0050.827932
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2121.1711394
X-RAY DIFFRACTIONr_long_range_B_refined2.7629.4312296
X-RAY DIFFRACTIONr_long_range_B_other2.5668.8252245
X-RAY DIFFRACTIONr_rigid_bond_restr7.25633720
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.57→1.611 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.151 110 -
Rwork0.054 2068 -
obs--95.57 %

+
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