[English] 日本語
Yorodumi
- PDB-4k4b: X-ray crystal structure of E. coli YdiI complexed with undeca-2-o... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4k4b
TitleX-ray crystal structure of E. coli YdiI complexed with undeca-2-one-CoA
ComponentsEsterase YdiI
KeywordsHYDROLASE / Hotdog fold / thioesterase
Function / homology
Function and homology information


1,4-dihydroxy-2-naphthoyl-CoA hydrolase / acyl-CoA hydrolase activity / 1,4-dihydroxy-2-naphthoyl-CoA thioesterase activity / menaquinone biosynthetic process / hydrolase activity / cytosol
Similarity search - Function
1,4-dihydroxy-2-naphthoyl-CoA hydrolase, MenI / Phenylacetic acid degradation-related domain / Thioesterase domain / Thioesterase superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
undeca-2-one coenzyme A / 1,4-dihydroxy-2-naphthoyl-CoA hydrolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRu, W. / Farelli, J.D. / Dunaway-Mariano, D. / Allen, K.N.
CitationJournal: Biochemistry / Year: 2014
Title: Structure and Catalysis in the Escherichia coli Hotdog-fold Thioesterase Paralogs YdiI and YbdB.
Authors: Wu, R. / Latham, J.A. / Chen, D. / Farelli, J. / Zhao, H. / Matthews, K. / Allen, K.N. / Dunaway-Mariano, D.
History
DepositionApr 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Esterase YdiI
B: Esterase YdiI
C: Esterase YdiI
D: Esterase YdiI
E: Esterase YdiI
F: Esterase YdiI
G: Esterase YdiI
H: Esterase YdiI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,96723
Polymers119,7308
Non-polymers12,23615
Water15,763875
1
A: Esterase YdiI
B: Esterase YdiI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7117
Polymers29,9332
Non-polymers3,7795
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-31 kcal/mol
Surface area13860 Å2
MethodPISA
2
C: Esterase YdiI
D: Esterase YdiI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8044
Polymers29,9332
Non-polymers1,8722
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-18 kcal/mol
Surface area13610 Å2
MethodPISA
3
E: Esterase YdiI
F: Esterase YdiI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7117
Polymers29,9332
Non-polymers3,7795
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-27 kcal/mol
Surface area14990 Å2
MethodPISA
4
G: Esterase YdiI
H: Esterase YdiI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7405
Polymers29,9332
Non-polymers2,8073
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-14 kcal/mol
Surface area14480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.970, 68.577, 81.144
Angle α, β, γ (deg.)78.93, 84.69, 76.46
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Esterase YdiI


Mass: 14966.271 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b1686, JW1676, ydiI, YdiL / Plasmid: pET-23a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: P77781, Hydrolases; Acting on ester bonds
#2: Chemical
ChemComp-UOQ / undeca-2-one coenzyme A


Mass: 935.810 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C32H56N7O17P3S
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 875 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsUNDECAN-2-ONE-COA (UOQ) WAS SYNTHESIZED TO SERVE AS STABLE KETO-THIOETHER (O=C-CH2-S) ANALOGS OF ...UNDECAN-2-ONE-COA (UOQ) WAS SYNTHESIZED TO SERVE AS STABLE KETO-THIOETHER (O=C-CH2-S) ANALOGS OF THE CORRESPONDING THIOESTER SUBSTRATES DECANOYL-COA. THE BONDS IN THIS INHIBITOR ARE NOT CLEAVED BY THE ENZYME AND IT HAS BEEN SHOWN TO BE A COMPETITIVE INHIBITOR. THOSE ATOMS IN THE INHIBITOR MOLECULE WITH POOR/NO DENSITY HAVE BEEN ASSIGNED AS OCC = 0 SO THAT THE MODEL IS NOT FRAGMENTED IN THE STRUCTURE

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.09 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.18 M MAGNESIUM ACETATE, 0.07-0.08 M SODIUM CACODYLATE, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Jul 9, 2009
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→33.886 Å / Num. obs: 87554 / Redundancy: 8.2 %

-
Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.8_1069)refinement
PROTEUM PLUSPLUSdata reduction
PROTEUM PLUSPLUSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1SBK

1sbk


Resolution: 1.9→33.886 Å / SU ML: 0.18 / σ(F): 1.97 / Phase error: 22.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2163 4149 5.04 %
Rwork0.169 --
obs0.1714 87554 93.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→33.886 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8368 0 782 875 10025
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089896
X-RAY DIFFRACTIONf_angle_d1.30813481
X-RAY DIFFRACTIONf_dihedral_angle_d27.2854391
X-RAY DIFFRACTIONf_chiral_restr0.0781381
X-RAY DIFFRACTIONf_plane_restr0.0041671
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.92160.25241250.20792385X-RAY DIFFRACTION79
1.9216-1.94420.22321290.20982376X-RAY DIFFRACTION81
1.9442-1.96790.27911290.20512447X-RAY DIFFRACTION82
1.9679-1.99280.28521320.20252484X-RAY DIFFRACTION84
1.9928-2.0190.24831510.1952530X-RAY DIFFRACTION85
2.019-2.04670.29221420.18722531X-RAY DIFFRACTION87
2.0467-2.07590.25011480.18192728X-RAY DIFFRACTION89
2.0759-2.10690.22431260.17652550X-RAY DIFFRACTION89
2.1069-2.13980.24451270.16972778X-RAY DIFFRACTION91
2.1398-2.17490.21031490.16712684X-RAY DIFFRACTION91
2.1749-2.21240.23481370.16652732X-RAY DIFFRACTION92
2.2124-2.25260.21651330.16632743X-RAY DIFFRACTION93
2.2526-2.29590.24011370.17572778X-RAY DIFFRACTION93
2.2959-2.34280.25051520.17992798X-RAY DIFFRACTION94
2.3428-2.39370.2151530.1682792X-RAY DIFFRACTION95
2.3937-2.44940.23391470.17422875X-RAY DIFFRACTION95
2.4494-2.51060.22171570.18012849X-RAY DIFFRACTION96
2.5106-2.57850.24881440.17662845X-RAY DIFFRACTION96
2.5785-2.65430.23181500.17412906X-RAY DIFFRACTION97
2.6543-2.740.23381550.17152936X-RAY DIFFRACTION98
2.74-2.83780.24011400.17952934X-RAY DIFFRACTION99
2.8378-2.95140.23261640.17042920X-RAY DIFFRACTION99
2.9514-3.08560.22191440.17012969X-RAY DIFFRACTION99
3.0856-3.24820.20451580.16712958X-RAY DIFFRACTION99
3.2482-3.45150.20421680.15392908X-RAY DIFFRACTION99
3.4515-3.71770.1621780.14092912X-RAY DIFFRACTION99
3.7177-4.09130.17551380.14632979X-RAY DIFFRACTION99
4.0913-4.6820.16951730.13572943X-RAY DIFFRACTION100
4.682-5.89370.1981600.1672978X-RAY DIFFRACTION100
5.8937-33.8860.21461710.18912889X-RAY DIFFRACTION98

+
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