[English] 日本語
Yorodumi
- PDB-1vgq: Formyl-CoA transferase mutant Asp169 to Ala -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1vgq
TitleFormyl-CoA transferase mutant Asp169 to Ala
ComponentsFormyl-coenzyme A transferase
KeywordsTRANSFERASE / CoA-transferase / oxalate / oxalate degradation / intertwined / knotted fold / CAIB-BAIF family / CoA complex
Function / homology
Function and homology information


formyl-CoA transferase / formyl-CoA transferase activity / oxalate catabolic process / cytoplasm
Similarity search - Function
Formyl-CoA:oxalate CoA-transferase / formyl-coa transferase, domain 3 / Crotonobetainyl-coa:carnitine coa-transferase; domain 1 / CoA-transferase family III domain 3 superfamily / formyl-coa transferase, domain 3 / CoA-transferase family III / CoA-transferase family III domain 1 superfamily / CoA-transferase family III / Rossmann fold / 2-Layer Sandwich ...Formyl-CoA:oxalate CoA-transferase / formyl-coa transferase, domain 3 / Crotonobetainyl-coa:carnitine coa-transferase; domain 1 / CoA-transferase family III domain 3 superfamily / formyl-coa transferase, domain 3 / CoA-transferase family III / CoA-transferase family III domain 1 superfamily / CoA-transferase family III / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
OXIDIZED COENZYME A / Formyl-CoA:oxalate CoA-transferase
Similarity search - Component
Biological speciesOxalobacter formigenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.13 Å
AuthorsRicagno, S. / Jonsson, S. / Richards, N.G. / Lindqvist, Y.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Kinetic and mechanistic characterization of the formyl-CoA transferase from Oxalobacter formigenes
Authors: Jonsson, S. / Ricagno, S. / Lindqvist, Y. / Richards, N.G.
History
DepositionApr 28, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Nov 10, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 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: Formyl-coenzyme A transferase
B: Formyl-coenzyme A transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,9424
Polymers94,3752
Non-polymers1,5672
Water8,467470
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15410 Å2
ΔGint-96 kcal/mol
Surface area29100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.116, 151.116, 99.593
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

-
Components

#1: Protein Formyl-coenzyme A transferase / Formyl-CoA transferase


Mass: 47187.656 Da / Num. of mol.: 2 / Mutation: D169A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oxalobacter formigenes (bacteria) / Gene: FRC / Plasmid: pET9a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: O06644, formyl-CoA transferase
#2: Chemical ChemComp-CAO / OXIDIZED COENZYME A


Mass: 783.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O17P3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 470 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000, Mg chloride, Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.812 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 2, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.812 Å / Relative weight: 1
ReflectionResolution: 2.13→20.17 Å / Num. all: 61071 / Num. obs: 61071 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 31.3 Å2 / Rsym value: 0.091 / Net I/σ(I): 13.7
Reflection shellResolution: 2.13→2.24 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 7477 / Rsym value: 0.417 / % possible all: 81.9

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1P5R

1p5r


Resolution: 2.13→20.17 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.992 / SU ML: 0.103 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.185 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2019 3068 5 %RANDOM
Rwork0.171 ---
all0.172 57940 --
obs0.172 57940 98.24 %-
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: 30.873 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å20 Å2
2--0.34 Å20 Å2
3----0.68 Å2
Refinement stepCycle: LAST / Resolution: 2.13→20.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6620 0 98 470 7188
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0216867
X-RAY DIFFRACTIONr_bond_other_d0.0020.026130
X-RAY DIFFRACTIONr_angle_refined_deg1.4041.9679303
X-RAY DIFFRACTIONr_angle_other_deg0.817314323
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1155851
X-RAY DIFFRACTIONr_chiral_restr0.0790.2995
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027658
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021340
X-RAY DIFFRACTIONr_nbd_refined0.1960.21464
X-RAY DIFFRACTIONr_nbd_other0.2280.27236
X-RAY DIFFRACTIONr_nbtor_other0.0840.23815
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2419
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1310.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2290.226
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1360.212
X-RAY DIFFRACTIONr_mcbond_it0.5861.54227
X-RAY DIFFRACTIONr_mcangle_it1.10426778
X-RAY DIFFRACTIONr_scbond_it1.49632640
X-RAY DIFFRACTIONr_scangle_it2.4674.52524
LS refinement shellResolution: 2.135→2.19 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.271 150
Rwork0.232 3361
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.55020.0522-0.27740.23050.03120.3822-0.035-0.0177-0.010.0707-0.02380.03220.0244-0.01130.05880.02970.01940.01050.0216-0.0080.0284-36.24421.9878.597
20.34680.0116-0.03040.30890.07470.3711-0.0315-0.0264-0.0111-0.00290.01190.04780.0301-0.02880.01970.02250.00950.00070.0184-0.00730.0319-34.22517.8850.702
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 4281 - 427
2X-RAY DIFFRACTION2BB2 - 4281 - 427

+
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