[English] 日本語
Yorodumi
- PDB-4o5t: Crystal structure of Diels-Alderase CE20 in complex with a produc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4o5t
TitleCrystal structure of Diels-Alderase CE20 in complex with a product analog
ComponentsDiisopropyl-fluorophosphatase
KeywordsDe Novo Protein / Hydrolase / protein engineering / computer-aided design / Diels-Alder reaction / enzyme design / directed evolution / substrate specificity / beta-propeller / helix-loop-helix / artificial catalyst / Diels-Alderase / catalyst for cycloaddition / enzyme-product analog complex'
Function / homology
Function and homology information


diisopropyl-fluorophosphatase / diisopropyl-fluorophosphatase activity / calcium ion binding
Similarity search - Function
: / SMP-30/Gluconolactonase/LRE-like region / SMP-30/Gluconolactonase/LRE-like region / TolB, C-terminal domain / Six-bladed beta-propeller, TolB-like / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
Chem-XDA / Diisopropyl-fluorophosphatase
Similarity search - Component
Biological speciesLoligo vulgaris (squid)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsBeck, T. / Preiswerk, N. / Mayer, C. / Hilvert, D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Impact of scaffold rigidity on the design and evolution of an artificial Diels-Alderase.
Authors: Preiswerk, N. / Beck, T. / Schulz, J.D. / Milovnik, P. / Mayer, C. / Siegel, J.B. / Baker, D. / Hilvert, D.
History
DepositionDec 20, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Diisopropyl-fluorophosphatase
B: Diisopropyl-fluorophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,5394
Polymers74,6002
Non-polymers9392
Water45025
1
A: Diisopropyl-fluorophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7702
Polymers37,3001
Non-polymers4691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Diisopropyl-fluorophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7702
Polymers37,3001
Non-polymers4691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.65, 128.94, 106.53
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Diisopropyl-fluorophosphatase / Diels-Alderase C20 / DFPase


Mass: 37300.098 Da / Num. of mol.: 2
Mutation: V13M, A21T, I33V, 36-PYVEVNGKPA-45 replaced by 36-SPLSEALINANSLAEAYEARSDA-58, R63H, I85S, A87I, K121N, R128C, E151G, Q162R, A186C, K223N, D245V, S284A, A285N, E301D, L322S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Loligo vulgaris (squid) / Production host: Escherichia coli (E. coli) / References: UniProt: Q7SIG4, EC: 3.1.8.2
#2: Chemical ChemComp-XDA / 4-{[2-(phosphonooxy)ethyl]carbamoyl}benzyl [(1R,6S)-6-(dimethylcarbamoyl)cyclohex-2-en-1-yl]carbamate


Mass: 469.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28N3O8P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 36-PEVEVNGKPA-45 IN UNP HAS BEEN REPLACED BY 36-SPLSEALINANSLAEAYEARSDA-58.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: protein solution (15.5 mg/mL, in 20 mM HEPES, pH 8.0, 150 mM NaCl), containing 20 mM product analog, was mixed with reservoir solution containing 20.0% w/v PEG 3350 and 0.2 M magnesium ...Details: protein solution (15.5 mg/mL, in 20 mM HEPES, pH 8.0, 150 mM NaCl), containing 20 mM product analog, was mixed with reservoir solution containing 20.0% w/v PEG 3350 and 0.2 M magnesium chloride , VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 12, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→43.08 Å / Num. obs: 13664 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 3.91 % / Rmerge(I) obs: 0.1124 / Net I/σ(I): 6.51
Reflection shellResolution: 2.9→3 Å / Redundancy: 3.82 % / Rmerge(I) obs: 0.7294 / Mean I/σ(I) obs: 1.03 / Num. unique all: 1311 / % possible all: 97.8

-
Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.7.0032refinement
XDSdata reduction
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4O5S

4o5s


Resolution: 2.9→43.08 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.885 / SU B: 28.068 / SU ML: 0.485 / Cross valid method: THROUGHOUT / ESU R Free: 0.526 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28758 655 4.9 %RANDOM
Rwork0.2279 ---
obs0.23077 12809 96.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 74.83 Å2
Baniso -1Baniso -2Baniso -3
1-4.72 Å20 Å2-0 Å2
2---1.86 Å2-0 Å2
3----2.86 Å2
Refinement stepCycle: LAST / Resolution: 2.9→43.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4718 0 64 25 4807
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194928
X-RAY DIFFRACTIONr_bond_other_d0.0010.024542
X-RAY DIFFRACTIONr_angle_refined_deg1.4281.956721
X-RAY DIFFRACTIONr_angle_other_deg0.7543.00410284
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1785645
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.2824.869191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.46515680
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7921511
X-RAY DIFFRACTIONr_chiral_restr0.0810.2736
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215774
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021145
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_it2.617.7292588
X-RAY DIFFRACTIONr_mcbond_other2.617.7282587
X-RAY DIFFRACTIONr_mcangle_it4.40111.5973231
X-RAY DIFFRACTIONr_mcangle_other4.40111.5983232
X-RAY DIFFRACTIONr_scbond_it2.2147.7522338
X-RAY DIFFRACTIONr_scbond_other2.2167.7562334
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.79411.5623485
X-RAY DIFFRACTIONr_long_range_B_refined9.17572.65820745
X-RAY DIFFRACTIONr_long_range_B_other9.17572.65720745
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.413 45 -
Rwork0.367 812 -
obs--86.04 %

+
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