[English] 日本語
Yorodumi
- PDB-4bs0: Crystal Structure of Kemp Eliminase HG3.17 E47N,N300D Complexed w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4bs0
TitleCrystal Structure of Kemp Eliminase HG3.17 E47N,N300D Complexed with Transition State Analog 6-Nitrobenzotriazole
ComponentsKEMP ELIMINASE HG3.17
KeywordsLYASE/LYASE INHIBITOR / LYASE-LYASE INHIBITOR COMPLEX / COMPUTATIONAL PROTEIN DESIGN / PROTON TRANSFER / KEMP ELIMINATION / DIRECTED EVOLUTION / TRANSITION STATE TUNING / BOTTOM-UP ENZYME CONSTRUCTION / ELEMENTARY CHEMICAL STEP CATALYSIS
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 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel ...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 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
6-NITROBENZOTRIAZOLE / Endo-1,4-beta-xylanase
Similarity search - Component
Biological speciesTHERMOASCUS AURANTIACUS (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.09 Å
AuthorsBlomberg, R. / Kries, H. / Pinkas, D.M. / Mittl, P.R.E. / Gruetter, M.G. / Privett, H.K. / Mayo, S. / Hilvert, D.
CitationJournal: Nature / Year: 2013
Title: Precision is Essential for Efficient Catalysis in an Evolved Kemp Eliminase
Authors: Blomberg, R. / Kries, H. / Pinkas, D.M. / Mittl, P.R.E. / Gruetter, M.G. / Privett, H.K. / Mayo, S.L. / Hilvert, D.
History
DepositionJun 6, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Nov 27, 2013Group: Database references
Revision 2.0Dec 20, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: KEMP ELIMINASE HG3.17
B: KEMP ELIMINASE HG3.17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,6368
Polymers68,9242
Non-polymers7126
Water14,988832
1
A: KEMP ELIMINASE HG3.17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8184
Polymers34,4621
Non-polymers3563
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: KEMP ELIMINASE HG3.17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8184
Polymers34,4621
Non-polymers3563
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.080, 77.950, 98.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein KEMP ELIMINASE HG3.17 / ENDO-1 / 4-BETA-XYLANASE / XYLANASE / 1\ / 4-BETA-D-XYLAN XYLANOHYDROLASE


Mass: 34461.824 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: KEMP ELIMINASE HG-2 (PDB ID 3NYD) WITH MUTATION V6I, Q37K, K50Q, G82A, M84C, S89N, Q90F, T105I, A125T, T142N, T208M, S265T, F267M, W275A, R276F, T279S
Source: (gene. exp.) THERMOASCUS AURANTIACUS (fungus) / Description: ENGINEERED ENZYME / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD / References: UniProt: P23360, Lyases
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-6NT / 6-NITROBENZOTRIAZOLE


Mass: 164.122 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H4N4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 832 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.52 % / Description: NONE
Crystal growpH: 5.9
Details: 1.1 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE, PH 5.9, SEEDING

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.09→28.3 Å / Num. obs: 225765 / % possible obs: 93.1 % / Observed criterion σ(I): -3 / Redundancy: 12.2 % / Biso Wilson estimate: 9.99 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 32.1
Reflection shellResolution: 1.09→1.13 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 4.9 / % possible all: 57

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NYD

3nyd


Resolution: 1.09→28.339 Å / SU ML: 0.08 / σ(F): 1.92 / Phase error: 13.99 / Stereochemistry target values: LS_WUNIT_K1
Details: THE MAXIMUM-LIKELIHOOD TARGET FUNCTION WAS USED WITH OPTIMIZED STEREOCHEMICAL AND ATOMIC-DISPLACEMENT PARAMETER RESTRAINTS FOR THE MAJORITY OF THE REFINEMENT. IN THE FINAL STAGE, THE LIGAND ...Details: THE MAXIMUM-LIKELIHOOD TARGET FUNCTION WAS USED WITH OPTIMIZED STEREOCHEMICAL AND ATOMIC-DISPLACEMENT PARAMETER RESTRAINTS FOR THE MAJORITY OF THE REFINEMENT. IN THE FINAL STAGE, THE LIGAND AS WELL AS THE CATALYTIC RESIDUES ASP127 AND GLN50 FOR THE A-CHAIN WERE REFINED UNRESTRAINED, USING THE LEAST SQUARES TARGET FUNCTION.
RfactorNum. reflection% reflection
Rfree0.1452 11399 5.1 %
Rwork0.1241 --
obs0.1252 225746 93.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: PHENIX V1.8.2-1309
Displacement parametersBiso mean: 14.13 Å2
Refinement stepCycle: LAST / Resolution: 1.09→28.339 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4556 0 44 832 5432
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0157340
X-RAY DIFFRACTIONf_angle_d1.30810051
X-RAY DIFFRACTIONf_dihedral_angle_d12.4422624
X-RAY DIFFRACTIONf_chiral_restr0.0741107
X-RAY DIFFRACTIONf_plane_restr0.0081335
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.09-1.10240.20221930.18883729X-RAY DIFFRACTION49
1.1024-1.11540.21682330.18564272X-RAY DIFFRACTION56
1.1154-1.1290.22132630.17594930X-RAY DIFFRACTION65
1.129-1.14330.20033000.16615462X-RAY DIFFRACTION72
1.1433-1.15830.2073260.15846147X-RAY DIFFRACTION80
1.1583-1.17420.18323370.15856678X-RAY DIFFRACTION88
1.1742-1.19090.19724040.15777081X-RAY DIFFRACTION94
1.1909-1.20870.18223770.15297498X-RAY DIFFRACTION98
1.2087-1.22760.18153650.14737548X-RAY DIFFRACTION98
1.2276-1.24770.17293870.1417568X-RAY DIFFRACTION99
1.2477-1.26930.17624140.14237518X-RAY DIFFRACTION99
1.2693-1.29230.16863710.13247584X-RAY DIFFRACTION99
1.2923-1.31720.17664030.12777562X-RAY DIFFRACTION99
1.3172-1.34410.15544450.12627558X-RAY DIFFRACTION99
1.3441-1.37330.15824100.12577566X-RAY DIFFRACTION99
1.3733-1.40520.15323840.1237645X-RAY DIFFRACTION100
1.4052-1.44040.15264080.11797632X-RAY DIFFRACTION100
1.4404-1.47930.14144150.11377579X-RAY DIFFRACTION99
1.4793-1.52290.1443790.10627671X-RAY DIFFRACTION100
1.5229-1.5720.13244250.10467617X-RAY DIFFRACTION100
1.572-1.62820.14314410.10327668X-RAY DIFFRACTION100
1.6282-1.69340.13854080.10487665X-RAY DIFFRACTION100
1.6934-1.77040.14623940.10437685X-RAY DIFFRACTION100
1.7704-1.86380.12534220.10467665X-RAY DIFFRACTION100
1.8638-1.98050.12824120.10637689X-RAY DIFFRACTION100
1.9805-2.13340.13844180.10817729X-RAY DIFFRACTION100
2.1334-2.3480.12864020.10887751X-RAY DIFFRACTION100
2.348-2.68750.14114020.11857752X-RAY DIFFRACTION100
2.6875-3.38510.13864310.1297830X-RAY DIFFRACTION100
3.3851-28.34840.13344300.13938068X-RAY DIFFRACTION99

+
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