[English] 日本語
Yorodumi
- PDB-1pt8: Crystal structure of the yfdW gene product of E. coli, in complex... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1pt8
TitleCrystal structure of the yfdW gene product of E. coli, in complex with oxalate and acetyl-CoA
ComponentsHypothetical protein yfdW
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / CoA transferase / oxalate / acetyl-CoA / E. coli
Function / homology
Function and homology information


formyl-CoA transferase / formyl-CoA transferase activity / oxalate catabolic process / cellular response to acidic pH
Similarity search - Function
Formyl-CoA:oxalate CoA-transferase / : / formyl-coa transferase, domain 3 / Crotonobetainyl-coa:carnitine coa-transferase; domain 1 / formyl-coa transferase, domain 3 / CoA-transferase family III / CoA-transferase family III domain 1 superfamily / CoA-transferase family III domain 3 superfamily / CoA-transferase family III / Rossmann fold ...Formyl-CoA:oxalate CoA-transferase / : / formyl-coa transferase, domain 3 / Crotonobetainyl-coa:carnitine coa-transferase; domain 1 / formyl-coa transferase, domain 3 / CoA-transferase family III / CoA-transferase family III domain 1 superfamily / CoA-transferase family III domain 3 superfamily / CoA-transferase family III / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETYL COENZYME *A / OXALATE ION / Formyl-CoA:oxalate CoA-transferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Shigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsGruez, A. / Roig-Zamboni, V. / Valencia, C. / Campanacci, V. / Cambillau, C.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: The crystal structure of the Escherichia coli yfdW gene product reveals a new fold of two interlaced rings identifying a wide family of CoA transferases.
Authors: Gruez, A. / Roig-Zamboni, V. / Valencia, C. / Campanacci, V. / Cambillau, C.
History
DepositionJun 23, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Apr 3, 2024Group: 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_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_validate_close_contact / struct_conn

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hypothetical protein yfdW
B: Hypothetical protein yfdW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,08111
Polymers96,8262
Non-polymers2,2569
Water8,179454
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17550 Å2
ΔGint-96 kcal/mol
Surface area27680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.786, 146.786, 129.905
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

-
Components

#1: Protein Hypothetical protein yfdW


Mass: 48412.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli, Shigella flexneri / Genus: Escherichia, Shigella / Species: , / Strain: k12, k12 / Gene: YFDW OR B2374 OR SF2441 / Plasmid: pDest17 / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner(DE3)pLysS / References: UniProt: P69902
#2: Chemical ChemComp-OXL / OXALATE ION


Mass: 88.019 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2O4
#3: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 454 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.17 Å3/Da / Density % sol: 70.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: PEG600, cacodylate,oxalate, acethylCoA , pH 6.5, VAPOR DIFFUSION, temperature 298K
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
111 mg/mlprotein1drop
25 mMsodium HEPES1drop
3150 mM1dropNaCl
40.9 Mammonium phosphate1reservoir
50.1 Msodium HEPES1reservoirpH7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979257 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 9, 2003 / Details: mirrors
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979257 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 79388 / Num. obs: 79388 / % possible obs: 98.7 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rsym value: 0.114 / Net I/σ(I): 3.9
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 4 % / Mean I/σ(I) obs: 3 / Rsym value: 0.234 / % possible all: 98.3
Reflection
*PLUS
Rmerge(I) obs: 0.114
Reflection shell
*PLUS
% possible obs: 98.3 % / Redundancy: 0.234 % / Rmerge(I) obs: 0.03 / Mean I/σ(I) obs: 3

-
Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Apo-form

Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.585 / SU ML: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.163 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2037 6647 8.4 %RANDOM
Rwork0.18056 ---
all0.1825 79388 --
obs0.18251 72739 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 41.451 Å2
Baniso -1Baniso -2Baniso -3
1--1.65 Å2-0.83 Å20 Å2
2---1.65 Å20 Å2
3---2.48 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6440 0 144 454 7038
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0216720
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6231.9729123
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0325829
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.1010.2989
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025108
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2130.23289
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.2490
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.237
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1860.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.8481.54136
X-RAY DIFFRACTIONr_mcangle_it1.55926648
X-RAY DIFFRACTIONr_scbond_it2.66932584
X-RAY DIFFRACTIONr_scangle_it4.1624.52475
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.257 465
Rwork0.224 5284
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.204 / Rfactor Rwork: 0.177
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.016
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.6

+
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