[English] 日本語
Yorodumi
- PDB-6r2b: Crystal structure of the SucA domain of Mycobacterium smegmatis K... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6r2b
TitleCrystal structure of the SucA domain of Mycobacterium smegmatis KGD after soaking with succinylphosphonate
ComponentsMultifunctional 2-oxoglutarate metabolism enzyme
KeywordsOXIDOREDUCTASE / oxoglutarate dehydrogenase / TPP-dependent decarboxylase
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 / thiamine pyrophosphate binding / tricarboxylic acid cycle / magnesium ion binding
Similarity search - Function
TPP helical domain / 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 ...TPP helical domain / 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 / Helix Hairpins / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-QSP / Multifunctional 2-oxoglutarate metabolism enzyme
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.96 Å
AuthorsWagner, T. / Alzari, P.M. / Bellinzoni, M.
CitationJournal: J.Struct.Biol. / Year: 2019
Title: Conformational transitions in the active site of mycobacterial 2-oxoglutarate dehydrogenase upon binding phosphonate analogues of 2-oxoglutarate: From a Michaelis-like complex to ThDP adducts.
Authors: Wagner, T. / Boyko, A. / Alzari, P.M. / Bunik, V.I. / Bellinzoni, M.
History
DepositionMar 15, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 24, 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 / pdbx_struct_conn_angle / software / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _software.name / _struct_conn.pdbx_dist_value / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Multifunctional 2-oxoglutarate metabolism enzyme
B: Multifunctional 2-oxoglutarate metabolism enzyme
C: Multifunctional 2-oxoglutarate metabolism enzyme
D: Multifunctional 2-oxoglutarate metabolism enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)391,35816
Polymers388,6674
Non-polymers2,69112
Water24,5001360
1
A: Multifunctional 2-oxoglutarate metabolism enzyme
B: Multifunctional 2-oxoglutarate metabolism enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,6798
Polymers194,3332
Non-polymers1,3466
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11240 Å2
ΔGint-52 kcal/mol
Surface area57800 Å2
MethodPISA
2
C: Multifunctional 2-oxoglutarate metabolism enzyme
D: Multifunctional 2-oxoglutarate metabolism enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,6798
Polymers194,3332
Non-polymers1,3466
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11130 Å2
ΔGint-54 kcal/mol
Surface area57560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.120, 82.760, 162.970
Angle α, β, γ (deg.)98.55, 97.52, 102.18
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Multifunctional 2-oxoglutarate metabolism enzyme / 2-hydroxy-3-oxoadipate synthase / HOAS / 2-oxoglutarate carboxy-lyase / 2-oxoglutarate ...2-hydroxy-3-oxoadipate synthase / HOAS / 2-oxoglutarate carboxy-lyase / 2-oxoglutarate decarboxylase / Alpha-ketoglutarate decarboxylase / KGD / Alpha-ketoglutarate-glyoxylate carboligase


Mass: 97166.648 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: kgd, sucA, MSMEG_5049, MSMEI_4922 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0R2B1, 2-hydroxy-3-oxoadipate synthase, 2-oxoglutarate decarboxylase, oxoglutarate dehydrogenase (succinyl-transferring), dihydrolipoyllysine-residue succinyltransferase
#2: Chemical
ChemComp-QSP / (4~{S})-4-[(2~{R})-3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-5-[2-[oxidanyl(phosphonooxy)phosphoryl]oxyethyl]-2~{H}-1,3-thiazol-2-yl]-4-oxidanyl-4-phosphono-butanoic acid


Mass: 608.391 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H27N4O13P3S
#3: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1360 / 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: 2.72 Å3/Da / Density % sol: 54.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 60% MPD, 22.5 mM Na acetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97895 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97895 Å / Relative weight: 1
ReflectionResolution: 1.96→158.88 Å / Num. obs: 284499 / % possible obs: 97.1 % / Redundancy: 2.9 % / Biso Wilson estimate: 28.78 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.052 / Net I/σ(I): 8.6
Reflection shellResolution: 1.96→2 Å / Redundancy: 3 % / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 14077 / CC1/2: 0.8 / Rpim(I) all: 0.344 / % possible all: 96.6

-
Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
autoPROCdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2YID

2yid


Resolution: 1.96→158.87 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.919 / SU R Cruickshank DPI: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.175 / SU Rfree Blow DPI: 0.148 / SU Rfree Cruickshank DPI: 0.151
RfactorNum. reflection% reflectionSelection details
Rfree0.245 14368 5.05 %RANDOM
Rwork0.228 ---
obs0.229 284471 97.1 %-
Displacement parametersBiso mean: 33.33 Å2
Baniso -1Baniso -2Baniso -3
1--4.8456 Å2-0.54 Å21.0042 Å2
2--0.3602 Å20.6368 Å2
3---4.4854 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: 1 / Resolution: 1.96→158.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26203 0 156 1360 27719
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0126915HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9836506HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d12528SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes4708HARMONIC5
X-RAY DIFFRACTIONt_it26915HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.44
X-RAY DIFFRACTIONt_other_torsion2.71
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion3455SEMIHARMONIC5
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_contact32750SEMIHARMONIC4
LS refinement shellResolution: 1.96→1.98 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2531 276 4.85 %
Rwork0.2131 5414 -
all0.215 5690 -
obs--93.63 %
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)
10.3626-0.00490.07480.66680.15460.3904-0.00190.0497-0.0516-0.1597-0.00970.04110.13080.0530.01170.10030.0677-0.0419-0.118-0.0328-0.10461.9884-17.0857-17.9879
20.4570.0312-0.0330.6273-0.15320.5449-0.0017-0.04360.13140.0351-0.0256-0.1378-0.11440.13660.0274-0.00050.0261-0.0428-0.0887-0.0395-0.031418.037319.18453.4342
30.3147-0.22270.13460.5028-0.03430.68170.00790.00370.0689-0.0733-0.00030.1126-0.0813-0.0945-0.00760.02180.0842-0.0589-0.1123-0.0079-0.0281-22.189414.1125-5.0827
40.31870.01430.05970.4317-0.09430.7051-0.0008-0.0675-0.00970.1060.01510.02730.06630.0487-0.01430.0640.0846-0.0312-0.0878-0.0217-0.09381.041-12.654422.9294
50.1820.00350.16820.68780.07280.76-0.0261-0.01420.10920.04670.0318-0.0737-0.1210.0545-0.0057-0.00030.0451-0.0355-0.1143-0.0449-0.015527.519849.4821-65.7263
60.3794-0.07390.0410.37920.15980.77250.03860.0751-0.0167-0.1004-0.017-0.0210.0848-0.0192-0.02160.05060.0611-0.0257-0.0932-0.0198-0.079817.341215.5885-94.2318
70.4046-0.09160.16810.5915-0.00980.4566-0.0088-0.047-0.04650.10580.0148-0.04070.1785-0.0072-0.0060.07040.0712-0.041-0.103-0.0026-0.092618.081610.9419-53.6501
80.5814-0.1447-0.09840.59830.22060.74070.01110.03370.0362-0.0136-0.06320.1538-0.0422-0.22440.0521-0.06030.0702-0.0264-0.0288-0.0232-0.0425-11.22737.6346-74.8386
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|362 - A|827}
2X-RAY DIFFRACTION2{A|830 - A|1227}
3X-RAY DIFFRACTION3{B|365 - B|810}
4X-RAY DIFFRACTION4{B|811 - B|1227}
5X-RAY DIFFRACTION5{C|365 - C|810}
6X-RAY DIFFRACTION6{C|811 - C|1227}
7X-RAY DIFFRACTION7{D|367 - D|827}
8X-RAY DIFFRACTION8{D|830 - D|1227}

+
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