[English] 日本語
Yorodumi
- PDB-7cc4: A biodegradable plastic-degrading cutinase-like enzyme from the p... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7cc4
TitleA biodegradable plastic-degrading cutinase-like enzyme from the phyllosphere yeast Pseudozyma antarctica
ComponentsCutinase-like enzyme
KeywordsHYDROLASE / cutinase-like enzyme / biodegradable plastic degrading enzyme / alpha/beta hydrolase fold
Function / homology
Function and homology information


carboxylic ester hydrolase activity
Similarity search - Function
Cutinase / Cutinase/acetylxylan esterase / Cutinase / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Cutinase-like enzyme
Similarity search - Component
Biological speciesPseudozyma antarctica (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSuzuki, K. / Watanabe, T. / Kitamoto, H.
CitationJournal: To Be Published
Title: A biodegradable plastic-degrading cutinase-like enzyme from the phyllosphere yeast Pseudozyma antarctica
Authors: Suzuki, K. / Watanabe, T. / Kitamoto, H.
History
DepositionJun 16, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 2.0Nov 18, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: atom_site / citation_author ...atom_site / citation_author / entity_src_gen / pdbx_nonpoly_scheme / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns_shell / software / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.aniso_B[1][1] / _refine.aniso_B[2][2] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc_free / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.overall_SU_B / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine_hist.d_res_low / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_ls_restr.dev_ideal / _refine_ls_restr.dev_ideal_target / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _reflns_shell.number_measured_all / _reflns_shell.pdbx_netI_over_sigmaI_obs / _software.classification / _software.name / _software.version / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Description: Model orientation/position / Provider: author / Type: Coordinate replacement
Revision 2.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cutinase-like enzyme
B: Cutinase-like enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7763
Polymers40,7532
Non-polymers231
Water3,657203
1
A: Cutinase-like enzyme


Theoretical massNumber of molelcules
Total (without water)20,3771
Polymers20,3771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8330 Å2
MethodPISA
2
B: Cutinase-like enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4002
Polymers20,3771
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-9 kcal/mol
Surface area8520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.150, 61.596, 109.937
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Cutinase-like enzyme


Mass: 20376.658 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudozyma antarctica (fungus) / Gene: PaCLE1, CLE1, PSANT_00437 / Production host: Moesziomyces antarcticus (fungus) / Strain (production host): GB-4(0)-X14 / References: UniProt: S6BC01
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.84 Å3/Da / Density % sol: 33.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, TRIS hydrochloride, Sodium acetate trihydrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 25, 2017
RadiationMonochromator: Numerical link type Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→31.51 Å / Num. obs: 20991 / % possible obs: 99.9 % / Redundancy: 12.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.045 / Rrim(I) all: 0.16 / Net I/σ(I): 13
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.0512.80.4191928715080.9610.1210.4376.499.4
8.94-31.4911.30.0531632810.9950.0150.05222.798.1

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
xia20.6.2data reduction
MOLREP2.0.229phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CZQ

2czq


Resolution: 2→31.5 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.907 / SU B: 3.961 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.211 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2162 1000 4.8 %RANDOM
Rwork0.165 ---
obs0.1674 19938 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 42.74 Å2 / Biso mean: 9.654 Å2 / Biso min: 1.29 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å20 Å20 Å2
2---0.3 Å20 Å2
3---1.02 Å2
Refinement stepCycle: final / Resolution: 2→31.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2846 0 1 203 3050
Biso mean--1.29 13.79 -
Num. residues----394
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132902
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172674
X-RAY DIFFRACTIONr_angle_refined_deg1.5331.643950
X-RAY DIFFRACTIONr_angle_other_deg1.4321.5766140
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8525392
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.06323.692130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.11215422
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6391512
X-RAY DIFFRACTIONr_chiral_restr0.0730.2398
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023464
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02680
LS refinement shellResolution: 2→2.051 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.222 66 -
Rwork0.173 1440 -
all-1506 -
obs--99.41 %

+
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://pdbjlc1.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