[English] 日本語
Yorodumi
- PDB-3h7l: CRYSTAL STRUCTURE OF ENDOGLUCANASE-RELATED PROTEIN FROM Vibrio pa... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3h7l
TitleCRYSTAL STRUCTURE OF ENDOGLUCANASE-RELATED PROTEIN FROM Vibrio parahaemolyticus
ComponentsENDOGLUCANASE
KeywordsHYDROLASE / ENDOGLUCANASE / DEHYDROGENASE / PSI-2 / NYSGXRC / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS
Function / homology
Function and homology information


cellulase activity / polysaccharide catabolic process
Similarity search - Function
Cellulase N-terminal ig-like domain / Cellulase, Ig-like domain / Glycoside hydrolase family 9 / Glycosyl hydrolase family 9 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Immunoglobulin E-set ...Cellulase N-terminal ig-like domain / Cellulase, Ig-like domain / Glycoside hydrolase family 9 / Glycosyl hydrolase family 9 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Immunoglobulin E-set / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Endoglucanase-related protein
Similarity search - Component
Biological speciesVibrio parahaemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsPatskovsky, Y. / Toro, R. / Morano, C. / Rutter, M. / Chang, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: CRYSTAL STRUCTURE OF ENDOGLUCANASE-RELATED PROTEIN FROM Vibrio parahaemolyticus
Authors: Patskovsky, Y. / Toro, R. / Morano, C. / Rutter, M. / Chang, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionApr 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ENDOGLUCANASE
B: ENDOGLUCANASE
C: ENDOGLUCANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,2938
Polymers199,8333
Non-polymers4605
Water16,394910
1
A: ENDOGLUCANASE
hetero molecules

A: ENDOGLUCANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,4064
Polymers133,2222
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_675x-y+1,-y+2,-z1
Buried area3100 Å2
ΔGint-17 kcal/mol
Surface area38240 Å2
MethodPISA
2
B: ENDOGLUCANASE
hetero molecules

C: ENDOGLUCANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,5906
Polymers133,2222
Non-polymers3684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665x-y+1,-y+1,-z1
Buried area3650 Å2
ΔGint-19 kcal/mol
Surface area38060 Å2
MethodPISA
3
B: ENDOGLUCANASE
C: ENDOGLUCANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,5906
Polymers133,2222
Non-polymers3684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)166.124, 166.124, 343.534
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-660-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
DetailsAuthor states that the biological assembly is probably homodimer. Assembly still remains more hypothetical than real, so any possible combinations may be considered at this point and included in the PDB deposition. Therefore, two type of dimer are indicated.

-
Components

#1: Protein ENDOGLUCANASE / Endoglucanase-related protein


Mass: 66610.852 Da / Num. of mol.: 3 / Mutation: Y87T, V132A, G368T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Gene: VP2484 / Production host: Escherichia coli (E. coli) / References: UniProt: Q87LX4
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 910 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.43 Å3/Da / Density % sol: 64.18 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 60% TACSIMATE, PH 7.0, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K

-
Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9789
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 21, 2009 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 124285 / % possible obs: 99.9 % / Observed criterion σ(I): -0.5 / Redundancy: 5.7 % / Rsym value: 0.199 / Net I/σ(I): 3.8
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 1.4 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
SHELXDphasing
REFMAC5.3.0034refinement
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.922 / SU B: 7.105 / SU ML: 0.159 / Cross valid method: THROUGHOUT / ESU R: 0.213 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23164 3724 3 %RANDOM
Rwork0.18536 ---
obs0.18676 120045 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.74 Å2
Baniso -1Baniso -2Baniso -3
1--1.66 Å2-0.83 Å20 Å2
2---1.66 Å20 Å2
3---2.49 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13817 0 30 910 14757
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02114265
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2421.9219368
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.13551747
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.95724.807776
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.965152273
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4611568
X-RAY DIFFRACTIONr_chiral_restr0.0980.22006
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211268
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.160.37057
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.59814
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.51685
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1350.365
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.529
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.43428770
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.963313733
X-RAY DIFFRACTIONr_scbond_it7.27146315
X-RAY DIFFRACTIONr_scangle_it9.55665624
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 4558 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
loose positional0.265
loose positional0.260
loose positional0.270
loose thermal12.8310
loose thermal7.740
loose thermal7.70
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 275 -
Rwork0.31 8596 -
obs--99.62 %

+
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