[English] 日本語
Yorodumi
- PDB-3zhr: Crystal structure of the H747A mutant of the SucA domain of Mycob... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3zhr
TitleCrystal structure of the H747A mutant of the SucA domain of Mycobacterium smegmatis KGD showing the active site lid closed
ComponentsMULTIFUNCTIONAL 2-OXOGLUTARATE METABOLISM ENZYME
KeywordsOXIDOREDUCTASE / E1O
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
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
THIAMINE DIPHOSPHATE / Multifunctional 2-oxoglutarate metabolism enzyme
Similarity search - Component
Biological speciesMYCOBACTERIUM SMEGMATIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWagner, T. / Barilone, N. / Bellinzoni, M. / Alzari, P.M.
CitationJournal: Biochem.J. / Year: 2014
Title: A Dual Conformation of the Post-Decarboxylation Intermediate is Associated with Distinct Enzyme States in Mycobacterial Alpha-Ketoglutarate Decarboxylase (Kgd).
Authors: Wagner, T. / Barilone, N. / Alzari, P.M. / Bellinzoni, M.
History
DepositionDec 24, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Database references
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: 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)390,83020
Polymers388,3984
Non-polymers2,43116
Water21,1681175
1
A: MULTIFUNCTIONAL 2-OXOGLUTARATE METABOLISM ENZYME
B: MULTIFUNCTIONAL 2-OXOGLUTARATE METABOLISM ENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,41510
Polymers194,1992
Non-polymers1,2168
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12900 Å2
ΔGint-109.9 kcal/mol
Surface area54440 Å2
MethodPISA
2
C: MULTIFUNCTIONAL 2-OXOGLUTARATE METABOLISM ENZYME
D: MULTIFUNCTIONAL 2-OXOGLUTARATE METABOLISM ENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,41510
Polymers194,1992
Non-polymers1,2168
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12770 Å2
ΔGint-109.3 kcal/mol
Surface area54360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.970, 83.450, 159.670
Angle α, β, γ (deg.)99.64, 98.82, 100.98
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.2144, 0.0711, 0.9741), (0.0706, -0.9936, 0.088), (0.9742, 0.0877, 0.2081)45.6472, 4.9379, -37.1877
2given(-0.9285, -0.3713, -0.0017), (-0.3714, 0.9285, 0.0017), (0.0009, 0.0023, -1)-0.1869, 0.1216, 0.6078
3given(0.1729, 0.1513, -0.9732), (0.3085, -0.9467, -0.0924), (-0.9354, -0.2843, -0.2104)46.2734, 4.9911, -37.1625

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
MULTIFUNCTIONAL 2-OXOGLUTARATE METABOLISM ENZYME / 2-HYDROXY-3-OXOADIPATE SYNTHASE / HOA SYNTHASE / HOAS / 2-OXOGLUTARATE CARBOXY-LYASE / 2- ...2-HYDROXY-3-OXOADIPATE SYNTHASE / HOA SYNTHASE / HOAS / 2-OXOGLUTARATE CARBOXY-LYASE / 2-OXOGLUTARATE DECARBOXYLASE / ALPHA-KETOGLUTARATE DECARBOXYLASE / KG DECARBOXYLASE / KGD / ALPHA-KETOGLUTARATE-GLYOXYLATE CARBOLIGASE / 2-OXOGLUTARATE DEHYDROGENASE E1 COMPONENT / ODH E1 COMPONENT / ALPHA-KETOGLUTARATE DEHYDROGENASE E1 COMPONENT / KDH E1 COMPONENT / DIHYDROLIPOYLLYSINE-RESIDUE SUCCINYLTRANSFERASE COMPONENT OF 2-OXOGLUTARATE DEHYDROGENASE COMPLEX / 2-OXOGLUTARATE DEHYDROGENASE COMPLEX E2 COMPONENT / ODH E2 COMPONENT / OGDC-E2 / DIHYDROLIPOAMIDE SUCCINYLTRANSFERASE


Mass: 97099.586 Da / Num. of mol.: 4 / Fragment: SUCA-LIKE CATALYTIC DOMAIN, RESIDUES 361-1227 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM SMEGMATIS (bacteria) / Strain: MC2_155 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS
References: UniProt: A0R2B1, 2-hydroxy-3-oxoadipate synthase, 2-oxoglutarate decarboxylase, oxoglutarate dehydrogenase (succinyl-transferring), dihydrolipoyllysine-residue succinyltransferase

-
Non-polymers , 5 types, 1191 molecules

#2: Chemical
ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#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: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1175 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsN-TER FIRST GLYCINE 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: 2.61 Å3/Da / Density % sol: 52.9 % / Description: NONE
Crystal growpH: 7.6 / Details: 52% MPD, 20 MM NA ACETATE, pH 7.6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9537
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 18, 2011 / Details: KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS
RadiationMonochromator: SI(111) CHANNEL-CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.1→48.75 Å / Num. obs: 221700 / % possible obs: 96.6 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 33.14 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.7
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 1.9 / % possible all: 92.1

-
Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YIC

2yic


Resolution: 2.1→30.75 Å / Cor.coef. Fo:Fc: 0.9421 / Cor.coef. Fo:Fc free: 0.9309 / SU R Cruickshank DPI: 0.184 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.177 / SU Rfree Blow DPI: 0.144 / SU Rfree Cruickshank DPI: 0.148
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=MG CA. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=26667. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=MG CA. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=26667. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=8.
RfactorNum. reflection% reflectionSelection details
Rfree0.202 11121 5.02 %RANDOM
Rwork0.1801 ---
obs0.1812 221623 96.85 %-
Displacement parametersBiso mean: 38.93 Å2
Baniso -1Baniso -2Baniso -3
1--4.8417 Å2-1.1693 Å2-2.445 Å2
2--2.546 Å21.6927 Å2
3---2.2956 Å2
Refine analyzeLuzzati coordinate error obs: 0.263 Å
Refinement stepCycle: LAST / Resolution: 2.1→30.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25320 0 144 1175 26639
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0126006HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9935288HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d12003SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes661HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3851HARMONIC5
X-RAY DIFFRACTIONt_it26006HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.39
X-RAY DIFFRACTIONt_other_torsion2.63
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion3373SEMIHARMONIC5
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_contact31896SEMIHARMONIC4
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 798 5.16 %
Rwork0.2134 14657 -
all0.2149 15455 -
obs--96.85 %
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)
10.6446-0.22770.05631.2037-0.13170.9674-0.00350.04630.1238-0.03350.04120.296-0.0679-0.107-0.0377-0.13530.1134-0.0382-0.10080.02410.009-16.588815.1743-46.2788
20.4812-0.09830.12940.638-0.17720.8065-0.0095-0.0923-0.04780.1620.02270.05640.14470.0713-0.01320.04740.14770.0189-0.0550.0089-0.13196.5009-15.2439-19.7965
30.78490.01520.03380.96340.12310.67410.00120.2394-0.1258-0.2393-0.0180.06840.22690.07130.01690.01650.1113-0.0316-0.0514-0.0396-0.15255.4454-15.3547-61.436
40.64210.0788-0.1160.9946-0.29880.5849-0.0122-0.05470.16880.1263-0.0138-0.2077-0.11140.16420.0261-0.10290.0837-0.0356-0.0132-0.0103-0.050223.85318.8184-36.3228
50.5515-0.10090.0260.96460.19940.8797-0.0543-0.06970.25360.06660.058-0.2084-0.1370.0788-0.0037-0.06150.0388-0.0769-0.1221-0.0405-0.0039.113720.344446.6021
60.5407-0.0462-0.00140.6150.10010.78210.00590.0998-0.0514-0.1730.0053-0.06340.1584-0.004-0.01120.05050.0364-0.0001-0.072-0.0094-0.1186-0.5656-16.74120.3282
71.0843-0.22850.09080.8196-0.170.6441-0.0672-0.2554-0.10780.17470.0496-0.07680.1884-0.0260.01760.01790.0717-0.0381-0.04930.0444-0.16570.4653-16.69461.8893
80.7738-0.1863-0.15830.85920.10690.8135-0.02480.02530.0487-0.03850.01170.1938-0.0386-0.28760.0131-0.12520.0575-0.03990.02070.0162-0.0762-29.34988.277836.9042
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 366-810
2X-RAY DIFFRACTION2CHAIN A AND RESID 831-1227
3X-RAY DIFFRACTION3CHAIN B AND RESID 363-810
4X-RAY DIFFRACTION4CHAIN B AND RESID 831-1227
5X-RAY DIFFRACTION5CHAIN C AND RESID 365-810
6X-RAY DIFFRACTION6CHAIN C AND RESID 831-1227
7X-RAY DIFFRACTION7CHAIN D AND RESID 363-810
8X-RAY DIFFRACTION8CHAIN D AND RESID 831-1227

+
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