[English] 日本語
Yorodumi
- PDB-2xt6: Crystal structure of Mycobacterium smegmatis alpha-ketoglutarate ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2xt6
TitleCrystal structure of Mycobacterium smegmatis alpha-ketoglutarate decarboxylase homodimer (orthorhombic form)
Components2-OXOGLUTARATE DECARBOXYLASE
KeywordsLYASE / KDH / KGD
Function / homology
Function and homology information


2-hydroxy-3-oxoadipate synthase / 2-oxoglutarate decarboxylase / 2-oxoglutarate decarboxylase activity / 2-hydroxy-3-oxoadipate synthase activity / oxoglutarate dehydrogenase (succinyl-transferring) / oxoglutarate dehydrogenase (succinyl-transferring) activity / dihydrolipoyllysine-residue succinyltransferase / dihydrolipoyllysine-residue succinyltransferase activity / oxoglutarate dehydrogenase complex / thiamine pyrophosphate binding ...2-hydroxy-3-oxoadipate synthase / 2-oxoglutarate decarboxylase / 2-oxoglutarate decarboxylase activity / 2-hydroxy-3-oxoadipate synthase activity / oxoglutarate dehydrogenase (succinyl-transferring) / oxoglutarate dehydrogenase (succinyl-transferring) activity / dihydrolipoyllysine-residue succinyltransferase / dihydrolipoyllysine-residue succinyltransferase activity / oxoglutarate dehydrogenase complex / thiamine pyrophosphate binding / tricarboxylic acid cycle / magnesium ion binding / cytosol
Similarity search - Function
Multifunctional 2-oxoglutarate metabolism enzyme, C-terminal domain / Rossmann fold - #12470 / 2-oxoglutarate dehydrogenase E1 component, N-terminal domain / 2-oxoglutarate dehydrogenase N-terminus / Multifunctional 2-oxoglutarate metabolism enzyme, C-terminal / Multifunctional 2-oxoglutarate metabolism enzyme, C-terminal domain superfamily / 2-oxoglutarate dehydrogenase C-terminal / 2-oxoglutarate dehydrogenase E1 component / Dehydrogenase, E1 component / Dehydrogenase E1 component ...Multifunctional 2-oxoglutarate metabolism enzyme, C-terminal domain / Rossmann fold - #12470 / 2-oxoglutarate dehydrogenase E1 component, N-terminal domain / 2-oxoglutarate dehydrogenase N-terminus / Multifunctional 2-oxoglutarate metabolism enzyme, C-terminal / Multifunctional 2-oxoglutarate metabolism enzyme, C-terminal domain superfamily / 2-oxoglutarate dehydrogenase C-terminal / 2-oxoglutarate dehydrogenase E1 component / Dehydrogenase, E1 component / Dehydrogenase E1 component / 2-oxoacid dehydrogenase acyltransferase, catalytic domain / 2-oxoacid dehydrogenases acyltransferase (catalytic domain) / Transketolase-like, pyrimidine-binding domain / Transketolase, pyrimidine binding domain / Transketolase, pyrimidine binding domain / Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / Chloramphenicol acetyltransferase-like domain superfamily / Thiamin diphosphate-binding fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
THIAMINE DIPHOSPHATE / Multifunctional 2-oxoglutarate metabolism enzyme
Similarity search - Component
Biological speciesMYCOBACTERIUM SMEGMATIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 Å
AuthorsWagner, T. / Bellinzoni, M. / Wehenkel, A.M. / O'Hare, H.M. / Alzari, P.M.
CitationJournal: Chem.Biol. / Year: 2011
Title: Functional Plasticity and Allosteric Regulation of Alpha-Ketoglutarate Decarboxylase in Central Mycobacterial Metabolism.
Authors: Wagner, T. / Bellinzoni, M. / Wehenkel, A.M. / O'Hare, H.M. / Alzari, P.M.
History
DepositionOct 5, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2011Group: Database references / Version format compliance
Revision 1.2Dec 20, 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 / struct_site
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 / _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: 2-OXOGLUTARATE DECARBOXYLASE
B: 2-OXOGLUTARATE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,1728
Polymers248,1932
Non-polymers9796
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11170 Å2
ΔGint-86.1 kcal/mol
Surface area72570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.990, 247.720, 79.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9623, -0.2124, -0.1697), (-0.2111, 0.19, 0.9588), (-0.1714, 0.9585, -0.2277)
Vector: 31.9976, 63.7241, -72.1522)

-
Components

#1: Protein 2-OXOGLUTARATE DECARBOXYLASE / ALPHA-KETOGLUTARATE DECARBOXYLASE / 2-OXOGLUTARATE CARBOXY-LYASE


Mass: 124096.305 Da / Num. of mol.: 2 / Fragment: RESIDUES 116-1227
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM SMEGMATIS (bacteria) / Strain: MC2 155 / Plasmid: PET-28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: A0R2B1, 2-oxoglutarate decarboxylase
#2: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFIRST GLY RESIDUE IS A PURIFICATION TAG LEFTOVER (TEV CLEAVAGE SITE)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.3 Å3/Da / Density % sol: 62.7 % / Description: NONE
Crystal growpH: 7 / Details: 39% MPD, 100 MM HEPES, PH 7.0, 200 MM NACL

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.0332
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 26, 2009 / Details: KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS
RadiationMonochromator: CHANNEL CUT MONOCHROMATOR CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.74→82 Å / Num. obs: 79835 / % possible obs: 99.3 % / Observed criterion σ(I): 2.4 / Redundancy: 3.5 % / Biso Wilson estimate: 75.02 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.3
Reflection shellResolution: 2.74→2.89 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.4 / % possible all: 97.5

-
Processing

Software
NameVersionClassification
BUSTER-TNT2.9.3refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XT9

2xt9
PDB Unreleased entry


Resolution: 2.74→40.12 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.8741 / SU R Cruickshank DPI: 0.508 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.48 / SU Rfree Blow DPI: 0.267 / SU Rfree Cruickshank DPI: 0.274
RfactorNum. reflection% reflectionSelection details
Rfree0.2236 4017 5.05 %RANDOM
Rwork0.1854 ---
obs0.1874 79534 99.13 %-
Displacement parametersBiso mean: 70.04 Å2
Baniso -1Baniso -2Baniso -3
1-25.4159 Å20 Å20 Å2
2---9.113 Å20 Å2
3----16.303 Å2
Refine analyzeLuzzati coordinate error obs: 0.377 Å
Refinement stepCycle: LAST / Resolution: 2.74→40.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15727 0 56 119 15902
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0116094HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0921842HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d7384SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes401HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2392HARMONIC5
X-RAY DIFFRACTIONt_it16040HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.11
X-RAY DIFFRACTIONt_other_torsion2.95
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2110SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact18651SEMIHARMONIC4
LS refinement shellResolution: 2.74→2.81 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2937 294 5.23 %
Rwork0.2332 5324 -
all0.2364 5618 -
obs--99.13 %
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)
17.16020.0757-0.50331.30390.11350.238-0.08520.1840.8317-0.009-0.04710.1060.0836-0.11410.1323-0.06040.02720.0257-0.0887-0.05860.3696-40.192103.20621.998
21.0146-0.2429-0.29470.48870.35660.6818-0.01860.16930.4615-0.1252-0.00290.2284-0.1524-0.16690.0215-0.0479-0.0018-0.06280.0020.17570.0795-9.243289.5636-3.9736
31.59730.2896-0.17131.18460.1090.8994-0.08070.4002-0.1695-0.27030.1487-0.0817-0.09860.1372-0.0679-0.0754-0.1011-0.03180.07060.0341-0.310927.314266.4144-25.004
45.23032.1927-0.47672.10271.50341.6177-0.1921-0.54082.35070.14190.3085-0.74640.34790.0957-0.1164-0.34520.1321-0.3261-0.2474-0.23161.206941.3218109.33328.6535
52.41320.64570.64051.37550.29370.39010.0005-0.20580.20820.19860.0035-0.0007-0.0153-0.0679-0.004-0.0547-0.0501-0.01120.02450.0946-0.266522.214579.551616.3575
61.27890.1897-0.15460.63420.11630.60550.00820.038-0.52930.0435-0.02530.16520.0581-0.11550.0171-0.1148-0.0817-0.0654-0.07760.09770.0213-4.26246.6851-7.3845
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(A121 - A347)
2X-RAY DIFFRACTION2(A348 - A814)
3X-RAY DIFFRACTION3(A831 - A2003)
4X-RAY DIFFRACTION4(B128 - B347)
5X-RAY DIFFRACTION5(B348 - B810)
6X-RAY DIFFRACTION6(B832 - B2003)

+
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