[English] 日本語
Yorodumi
- PDB-7qjt: Crystal structure of a cutinase enzyme from Thermobifida cellulos... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7qjt
TitleCrystal structure of a cutinase enzyme from Thermobifida cellulosilytica TB100 (711)
Componentscutinase (711)
KeywordsHYDROLASE / plastic degradation
Biological speciesThermobifida cellulosilytica TB100 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsZahn, M. / Shakespeare, T.J. / Beckham, G.T. / McGeehan, J.E.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
UK Research and Innovation (UKRI)Research England E3 funding United Kingdom
CitationJournal: Nat Commun / Year: 2022
Title: Sourcing thermotolerant poly(ethylene terephthalate) hydrolase scaffolds from natural diversity
Authors: Erickson, E. / Gado, J.E. / Avilan, L. / Bratti, F. / Brizendine, R.K. / Cox, P.A. / Gill, R. / Graham, R. / Kim, D.J. / Konig, G. / Michener, W.E. / Poudel, S. / Ramirez, K.J. / ...Authors: Erickson, E. / Gado, J.E. / Avilan, L. / Bratti, F. / Brizendine, R.K. / Cox, P.A. / Gill, R. / Graham, R. / Kim, D.J. / Konig, G. / Michener, W.E. / Poudel, S. / Ramirez, K.J. / Shakespeare, T.J. / Zahn, M. / Boyd, E.S. / Payne, C.M. / DuBois, J.L. / Pickford, A.R. / Beckham, G.T. / McGeehan, J.E.
History
DepositionDec 17, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: cutinase (711)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5066
Polymers29,1461
Non-polymers3595
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint-17 kcal/mol
Surface area10720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.297, 109.297, 44.184
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-593-

HOH

21A-609-

HOH

31A-632-

HOH

-
Components

#1: Protein cutinase (711)


Mass: 29146.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobifida cellulosilytica TB100 (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Magnesium Chloride Hexahydrate, 0.1 M Tris pH 8.5, 20 % (w/v) PEG 8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.777→77.285 Å / Num. obs: 17061 / % possible obs: 87.1 % / Redundancy: 26.2 % / CC1/2: 0.992 / Rmerge(I) obs: 0.639 / Rpim(I) all: 0.126 / Net I/σ(I): 6.3
Reflection shellResolution: 1.777→1.965 Å / Redundancy: 22 % / Rmerge(I) obs: 3.127 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 855 / CC1/2: 0.615 / Rpim(I) all: 0.65 / % possible all: 64.3

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5zoa

5zoa


Resolution: 1.78→77.285 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.904 / SU B: 8.471 / SU ML: 0.132 / Cross valid method: FREE R-VALUE / ESU R: 0.218 / ESU R Free: 0.19
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2415 853 5.001 %
Rwork0.1817 16204 -
all0.185 --
obs-17057 64.969 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 18.271 Å2
Baniso -1Baniso -2Baniso -3
1-0.359 Å2-0 Å2-0 Å2
2--0.359 Å2-0 Å2
3----0.717 Å2
Refinement stepCycle: LAST / Resolution: 1.78→77.285 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2044 0 19 241 2304
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132115
X-RAY DIFFRACTIONr_bond_other_d0.0010.0141912
X-RAY DIFFRACTIONr_angle_refined_deg1.7771.6512884
X-RAY DIFFRACTIONr_angle_other_deg1.431.574408
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9065266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.15820.625112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.38515305
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.7441518
X-RAY DIFFRACTIONr_chiral_restr0.0810.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022418
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02494
X-RAY DIFFRACTIONr_nbd_refined0.2270.2462
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1970.21888
X-RAY DIFFRACTIONr_nbtor_refined0.1720.21017
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.2978
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2199
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0520.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1360.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2880.226
X-RAY DIFFRACTIONr_nbd_other0.2570.243
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1730.217
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0820.22
X-RAY DIFFRACTIONr_mcbond_it1.2761.5891067
X-RAY DIFFRACTIONr_mcbond_other1.2681.5881066
X-RAY DIFFRACTIONr_mcangle_it2.2182.3781332
X-RAY DIFFRACTIONr_mcangle_other2.2182.381333
X-RAY DIFFRACTIONr_scbond_it1.4941.7911047
X-RAY DIFFRACTIONr_scbond_other1.4941.7931048
X-RAY DIFFRACTIONr_scangle_it2.5382.6151552
X-RAY DIFFRACTIONr_scangle_other2.5372.6161553
X-RAY DIFFRACTIONr_lrange_it5.29220.0322450
X-RAY DIFFRACTIONr_lrange_other4.93919.2692380
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.78-1.8260.46510.254920.256191500.84.85640.237
1.826-1.8760.20760.2721670.2718310.7530.7779.44840.26
1.876-1.9310.374200.272740.27818200.7850.79416.15380.249
1.931-1.990.256330.2535200.25317570.8370.83231.47410.239
1.99-2.0550.322400.2787090.2816860.8270.83244.42470.261
2.055-2.1270.291500.2628630.26416640.8520.8454.86780.231
2.127-2.2070.321530.2349740.23815950.80.86664.38870.213
2.207-2.2980.274500.21910740.22115390.8140.87273.03440.193
2.298-2.40.276700.20611850.2114720.870.88785.25810.178
2.4-2.5170.237650.20512760.20714200.8990.90394.43660.174
2.517-2.6530.261640.1912810.19313600.8950.92198.89710.157
2.653-2.8130.221630.17112320.17412960.9150.94499.92280.144
2.813-3.0070.251610.16111450.16612060.9380.9511000.134
3.007-3.2480.166460.14410810.14511270.9520.9591000.121
3.248-3.5570.214640.1479950.15110590.9350.9591000.127
3.557-3.9760.203400.1529170.1549570.9470.9631000.136
3.976-4.5890.22430.1458120.1488550.9470.9711000.138
4.589-5.6150.224410.1727030.1757440.9440.961000.16
5.615-7.9210.269260.1945580.1975840.9490.9491000.18
7.921-77.2850.225170.1723460.1743630.960.9761000.176
Refinement TLS params.Method: refined / Origin x: -2.8901 Å / Origin y: 26.549 Å / Origin z: -5.7805 Å
111213212223313233
T0.0011 Å2-0.0009 Å2-0.0021 Å2-0.0023 Å20.0023 Å2--0.0269 Å2
L0.2824 °2-0.0059 °2-0.0888 °2-0.3098 °2-0.0747 °2--0.2621 °2
S-0.0014 Å °-0.006 Å °-0.0152 Å °0.0055 Å °0.0078 Å °0.0007 Å °-0.005 Å °-0.008 Å °-0.0064 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA1 - 267
2X-RAY DIFFRACTION1ALLA301

+
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