[English] 日本語
Yorodumi
- PDB-7k4v: Crystal structure of Kemp Eliminase HG3.17 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7k4v
TitleCrystal structure of Kemp Eliminase HG3.17
ComponentsEndo-1,4-beta-xylanase
KeywordsHYDROLASE / kemp elimination / directed evolution
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process
Similarity search - Function
Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Endo-1,4-beta-xylanase
Similarity search - Component
Biological speciesThermoascus aurantiacus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsPadua, R.A.P. / Otten, R. / Bunzel, A. / Nguyen, V. / Pitsawong, W. / Patterson, M. / Sui, S. / Perry, S.L. / Cohen, A.E. / Hilvert, D. / Kern, D.
Funding support United States, Switzerland, 11items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-FG02-05ER15699 United States
Damon Runyon Cancer Research FoundationDRG-2114-12 United States
Department of Energy (DOE, United States)DE-AC02-76SF00515 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103393 United States
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30 GM124169 United States
Department of Energy (DOE, United States)DE-AC02-05CH11231 United States
National Institutes of Health/Office of the DirectorS10OD021832 United States
Swiss National Science Foundation Switzerland
Other government Switzerland
National Science Foundation (NSF, United States)BioXFEL STC (1231306) United States
CitationJournal: Science / Year: 2020
Title: How directed evolution reshapes the energy landscape in an enzyme to boost catalysis.
Authors: Otten, R. / Padua, R.A.P. / Bunzel, H.A. / Nguyen, V. / Pitsawong, W. / Patterson, M. / Sui, S. / Perry, S.L. / Cohen, A.E. / Hilvert, D. / Kern, D.
History
DepositionSep 16, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 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
Revision 1.3Oct 30, 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: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3852
Polymers33,1901
Non-polymers1941
Water4,846269
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.190, 65.670, 71.570
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Endo-1,4-beta-xylanase / Xylanase / 1 / 4-beta-D-xylan xylanohydrolase / TAXI


Mass: 33190.457 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoascus aurantiacus (fungus) / Gene: XYNA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P23360, endo-1,4-beta-xylanase
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.74 Å3/Da / Density % sol: 29.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 25% (w/v) PEG 4,000, 100 mM MES, pH 6.5, and 200 mM magnesium chloride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9999 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.3→48.39 Å / Num. obs: 57517 / % possible obs: 99.39 % / Redundancy: 6.5 % / Biso Wilson estimate: 16 Å2 / CC1/2: 0.998 / Net I/σ(I): 9.8
Reflection shellResolution: 1.3→1.346 Å / Num. unique obs: 5622 / CC1/2: 0.319

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
Cootmodel building
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4bs0

4bs0


Resolution: 1.3→48.39 Å / SU ML: 0.1942 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.7753
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1756 3772 3.48 %
Rwork0.1586 104764 -
obs0.1592 108536 98.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.88 Å2
Refinement stepCycle: LAST / Resolution: 1.3→48.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2291 0 0 269 2560
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01562498
X-RAY DIFFRACTIONf_angle_d1.39383425
X-RAY DIFFRACTIONf_chiral_restr0.0943377
X-RAY DIFFRACTIONf_plane_restr0.0104459
X-RAY DIFFRACTIONf_dihedral_angle_d6.2263360
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.320.41721180.38953522X-RAY DIFFRACTION89.68
1.32-1.330.4251500.3843584X-RAY DIFFRACTION91.21
1.33-1.350.38361110.35443741X-RAY DIFFRACTION95.39
1.35-1.370.38021690.34873902X-RAY DIFFRACTION98.55
1.37-1.390.35071500.33233871X-RAY DIFFRACTION98.8
1.39-1.410.4131180.32423921X-RAY DIFFRACTION99.04
1.41-1.440.30911320.27533904X-RAY DIFFRACTION99.16
1.44-1.460.23441500.24963923X-RAY DIFFRACTION99.54
1.46-1.490.28361270.22583932X-RAY DIFFRACTION99.31
1.49-1.520.22081570.21433906X-RAY DIFFRACTION99.58
1.52-1.550.24471440.19573884X-RAY DIFFRACTION99.33
1.55-1.580.23021420.18923954X-RAY DIFFRACTION99.54
1.58-1.620.19491250.1863893X-RAY DIFFRACTION99.31
1.62-1.660.22721340.18153925X-RAY DIFFRACTION99.46
1.66-1.70.2111490.17693966X-RAY DIFFRACTION99.56
1.7-1.750.20671240.16313909X-RAY DIFFRACTION99.41
1.75-1.810.19841510.15573905X-RAY DIFFRACTION99.58
1.81-1.870.17631450.15383951X-RAY DIFFRACTION99.61
1.87-1.950.15631370.14663882X-RAY DIFFRACTION99.68
1.95-2.040.17781410.14233942X-RAY DIFFRACTION99.61
2.04-2.150.15731330.13843904X-RAY DIFFRACTION99.8
2.15-2.280.17521400.12933963X-RAY DIFFRACTION99.81
2.28-2.460.13761560.13233907X-RAY DIFFRACTION99.71
2.46-2.70.14481350.1353946X-RAY DIFFRACTION99.37
2.7-3.10.15021360.1343916X-RAY DIFFRACTION99.44
3.1-3.90.14911510.12533909X-RAY DIFFRACTION99.75
3.9-48.390.12661470.13633802X-RAY DIFFRACTION96.69

+
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