[English] 日本語
Yorodumi
- PDB-4zzp: Dictyostelium purpureum cellobiohydrolase Cel7A apo structure -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4zzp
TitleDictyostelium purpureum cellobiohydrolase Cel7A apo structure
ComponentsCELLULOSE 1,4-BETA-CELLOBIOSIDASE
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE / CELLOBIOHYDROLASE / CELLULASE
Function / homology
Function and homology information


culmination involved in sorocarp development / cellulose 1,4-beta-cellobiosidase (non-reducing end) / cellulose 1,4-beta-cellobiosidase activity / cellulose binding / cellulose catabolic process
Similarity search - Function
1,4-Beta-D-Glucan Cellobiohydrolase I; Chain A / Glycoside hydrolase, family 7, domain / Glycoside hydrolase, family 7 / Glycoside hydrolase family 7, catalytic domain superfamily / Glycosyl hydrolase family 7 / Distorted Sandwich / Concanavalin A-like lectin/glucanase domain superfamily / Mainly Beta
Similarity search - Domain/homology
cellulose 1,4-beta-cellobiosidase (non-reducing end)
Similarity search - Component
Biological speciesDICTYOSTELIUM PURPUREUM (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMomeni, M.H. / Hobdey, S.E. / Knott, B. / Beckham, G.T. / Stahlberg, J.
CitationJournal: Appl.Environ.Microbiol. / Year: 2016
Title: Biochemical and Structural Characterization of Two Dictyostelium Cellobiohydrolases from the Amoebozoa Kingdom Reveal a High Conservation between Distant Phylogenetic Trees of Life.
Authors: Hobdey, S.E. / Knott, B.C. / Haddad Momeni, M. / Taylor, L.E. / Borisova, A.S. / Podkaminer, K.K. / Vanderwall, T.A. / Himmel, M.E. / Decker, S.R. / Beckham, G.T. / Stahlberg, J.
History
DepositionApr 13, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Database references
Revision 2.0Mar 11, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Polymer sequence
Category: chem_comp / entity_poly ...chem_comp / entity_poly / pdbx_database_status / struct_conn
Item: _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can ..._chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CELLULOSE 1,4-BETA-CELLOBIOSIDASE
B: CELLULOSE 1,4-BETA-CELLOBIOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,6315
Polymers94,9682
Non-polymers6643
Water3,063170
1
A: CELLULOSE 1,4-BETA-CELLOBIOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9263
Polymers47,4841
Non-polymers4422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CELLULOSE 1,4-BETA-CELLOBIOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7052
Polymers47,4841
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.643, 85.185, 168.503
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein CELLULOSE 1,4-BETA-CELLOBIOSIDASE


Mass: 47483.922 Da / Num. of mol.: 2 / Fragment: SECRETED ENZYME, RESIDUES 19-457
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DICTYOSTELIUM PURPUREUM (eukaryote) / Plasmid: PTRENO / Production host: TRICHODERMA REESEI (fungus) / Strain (production host): QM6A / Variant (production host): AST 1116
References: UniProt: F0ZJZ1, cellulose 1,4-beta-cellobiosidase (reducing end)
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsPYROGLUTAMIC ACID (PCA): MODIFIED N-TERMINAL GLN SIDECHAIN N-ACETYL-D-GLUCOSAMINE (NAG): N-GLYCOSYLATION

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 42 % / Description: NONE
Crystal growpH: 7 / Details: 0.1 M SODIUM MALONATE PH 7.0, 12% W/V PEG 3350.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.87
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 18, 2014 / Details: SILICON TOROIDAL MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.7→46.9 Å / Num. obs: 22787 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Rmerge(I) obs: 0.25 / Net I/σ(I): 5.3
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3.2 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4D5J

4d5j


Resolution: 2.7→84.25 Å / Cor.coef. Fo:Fc: 0.884 / Cor.coef. Fo:Fc free: 0.797 / SU B: 18.448 / SU ML: 0.382 / Cross valid method: THROUGHOUT / ESU R Free: 0.485 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.31337 1144 5 %RANDOM
Rwork0.23459 ---
obs0.23853 21569 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.656 Å2
Baniso -1Baniso -2Baniso -3
1--0.81 Å20 Å20 Å2
2--2.29 Å20 Å2
3----1.48 Å2
Refinement stepCycle: LAST / Resolution: 2.7→84.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6608 0 42 170 6820
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.026860
X-RAY DIFFRACTIONr_bond_other_d0.0010.025974
X-RAY DIFFRACTIONr_angle_refined_deg1.2691.9439363
X-RAY DIFFRACTIONr_angle_other_deg0.733313830
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2395881
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.25325.796314
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.015151022
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1291518
X-RAY DIFFRACTIONr_chiral_restr0.060.21017
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0218030
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021548
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_it0.3161.6143504
X-RAY DIFFRACTIONr_mcbond_other0.3161.6143503
X-RAY DIFFRACTIONr_mcangle_it0.5872.4214378
X-RAY DIFFRACTIONr_mcangle_other0.5872.4214379
X-RAY DIFFRACTIONr_scbond_it0.1861.6013356
X-RAY DIFFRACTIONr_scbond_other0.1861.6013356
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.3492.3994979
X-RAY DIFFRACTIONr_long_range_B_refined1.46512.687749
X-RAY DIFFRACTIONr_long_range_B_other1.45312.7467694
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 87 -
Rwork0.248 1562 -
obs--99.64 %

+
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