[English] 日本語
Yorodumi
- PDB-2c31: CRYSTAL STRUCTURE OF OXALYL-COA DECARBOXYLASE IN COMPLEX WITH THE... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2c31
TitleCRYSTAL STRUCTURE OF OXALYL-COA DECARBOXYLASE IN COMPLEX WITH THE COFACTOR DERIVATIVE THIAMIN-2-THIAZOLONE DIPHOSPHATE AND ADENOSINE DIPHOSPHATE
ComponentsOXALYL-COA DECARBOXYLASE
KeywordsLYASE / OXALYL-COA DECARBOXYLASE / OXALATE / THIAMIN DIPHOSPHATE / FLAVOPROTEIN / THIAMINE PYROPHOSPHATE
Function / homology
Function and homology information


oxalyl-CoA decarboxylase / oxalyl-CoA decarboxylase activity / oxalate catabolic process / fatty acid alpha-oxidation / thiamine pyrophosphate binding / ADP binding / magnesium ion binding / identical protein binding
Similarity search - Function
Oxalyl-CoA decarboxylase / TPP-binding domain containing protein HACL1-like / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain / Thiamine pyrophosphate enzyme, N-terminal TPP binding domain / Thiamine pyrophosphate enzyme, C-terminal TPP-binding / Thiamine pyrophosphate enzyme, C-terminal TPP binding domain / Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / TPP-binding domain ...Oxalyl-CoA decarboxylase / TPP-binding domain containing protein HACL1-like / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain / Thiamine pyrophosphate enzyme, N-terminal TPP binding domain / Thiamine pyrophosphate enzyme, C-terminal TPP-binding / Thiamine pyrophosphate enzyme, C-terminal TPP binding domain / Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / TPP-binding domain / Thiamin diphosphate-binding fold / DHS-like NAD/FAD-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Chem-TZD / Oxalyl-CoA decarboxylase
Similarity search - Component
Biological speciesOXALOBACTER FORMIGENES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsBerthold, C.L. / Moussatche, P. / Richards, N.G.J. / Lindqvist, Y.
Citation
Journal: J.Biol.Chem. / Year: 2005
Title: Structural Basis for Activation of the Thiamin Diphosphate-Dependent Enzyme Oxalyl-Coa Decarboxylase by Adenosine Diphosphate.
Authors: Berthold, C.L. / Moussatche, P. / Richards, N.G.J. / Lindqvist, Y.
#1: Journal: Biochim.Biophys.Acta / Year: 2006
Title: Detection and Characterization of Merohedral Twinning in Crystals of Oxalyl-Coenzyme a Decarboxylase from Oxalobacter Formigenes.
Authors: Berthold, C.L. / Sidhu, H. / Ricagno, S. / Richards, N.G.J. / Lindqvist, Y.
History
DepositionOct 3, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2005Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: OXALYL-COA DECARBOXYLASE
B: OXALYL-COA DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,2838
Polymers121,5002
Non-polymers1,7846
Water11,854658
1
A: OXALYL-COA DECARBOXYLASE
B: OXALYL-COA DECARBOXYLASE
hetero molecules

A: OXALYL-COA DECARBOXYLASE
B: OXALYL-COA DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)246,56716
Polymers242,9994
Non-polymers3,56712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
MethodPQS
Unit cell
Length a, b, c (Å)124.300, 124.300, 151.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-1, -4.0E-5, 0.00211), (-5.0E-5, -0.99905, -0.04362), (0.00211, -0.04362, 0.99905)
Vector: 117.80213, -0.0752, -0.07706)

-
Components

#1: Protein OXALYL-COA DECARBOXYLASE / OXALYL-COENZYME A DECARBOXYLASE


Mass: 60749.867 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) OXALOBACTER FORMIGENES (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P40149, oxalyl-CoA decarboxylase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-TZD / 2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL TRIHYDROGEN DIPHOSPHATE / THIAMIN THIAZOLONE DIPHOSPHATE


Mass: 440.306 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H18N4O8P2S
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 658 / 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: 2.8 Å3/Da / Density % sol: 53.61 %
Description: ACETOHYDROXYACID SYNTHASE WAS USED AS TEMPLATE TO SOLVE AN APPROXIMATE INCOMPLETE NOT FULLY REFINED STRUCTURE OF OXALYL-COA DECARBOXYLASE IN A DIFFERENT SPACE GROUP TO 4.1 A RESOLUTION. ...Description: ACETOHYDROXYACID SYNTHASE WAS USED AS TEMPLATE TO SOLVE AN APPROXIMATE INCOMPLETE NOT FULLY REFINED STRUCTURE OF OXALYL-COA DECARBOXYLASE IN A DIFFERENT SPACE GROUP TO 4.1 A RESOLUTION. THIS LOW RESOLUTION MODEL WAS THEN USED FOR MOLECULAR REPLACE IN THIS DATA.
Crystal growpH: 6.5
Details: 27V/V % PEG 550MME, 100MM BIS-TRIS PH 6.5, 50MM CACL2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97565
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 14, 2004 / Details: SILICON TOROIDAL MIRROR COATED WITH RHODIUM
RadiationMonochromator: SILICON (1 1 1) CHANNEL- CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97565 Å / Relative weight: 1
ReflectionResolution: 1.73→29.24 Å / Num. obs: 140751 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Biso Wilson estimate: 21.13 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 17.9
Reflection shellResolution: 1.73→1.82 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3.8 / % possible all: 100

-
Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JSC

1jsc


Resolution: 1.73→29.2 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: LEAST SQUARES RESIDUAL FOR HEMIHEDRAL TWINNING
Details: THE PROTOCOLL FOR HEMIHEDRALLY TWINNED DATA WAS USED. THE R-VALUES SHOWN IN REMARK 3 ABOVE ARE FOR TWINNED DATA.
RfactorNum. reflection% reflectionSelection details
Rfree0.1749 12699 4.6 %RANDOM BUT WITH TWIN RELATED REFLECTIONS IN SAME SET
Rwork0.1505 ---
obs0.1505 272696 99.6 %-
Solvent computationSolvent model: CNS BULK SOLVENT MODEL / Bsol: 56.1554 Å2 / ksol: 0.357619 e/Å3
Displacement parametersBiso mean: 25.19 Å2
Baniso -1Baniso -2Baniso -3
1-2.81 Å22.18 Å20 Å2
2--2.81 Å20 Å2
3----5.63 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.73→29.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8157 0 110 658 8925
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006619
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.29298
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.73
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.9397
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.0521.5
X-RAY DIFFRACTIONc_mcangle_it1.6732
X-RAY DIFFRACTIONc_scbond_it1.8752
X-RAY DIFFRACTIONc_scangle_it2.792.5
LS refinement shellResolution: 1.73→1.79 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.278 1219
Rwork0.2523 26176

+
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://pdbjlvh1.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