[English] 日本語
Yorodumi
- PDB-2w8n: The crystal structure of the oxidized form of human SSADH -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2w8n
TitleThe crystal structure of the oxidized form of human SSADH
ComponentsSUCCINATE-SEMIALDEHYDE DEHYDROGENASE, MITOCHONDRIAL
KeywordsOXIDOREDUCTASE / MITOCHONDRION / TRANSIT PEPTIDE / DISEASE MUTATION / SSA / NAD / POLYMORPHISM / MITOCHONDRIA
Function / homology
Function and homology information


Degradation of GABA / succinate-semialdehyde dehydrogenase (NAD+) / succinate-semialdehyde dehydrogenase (NAD+) activity / succinate metabolic process / gamma-aminobutyric acid catabolic process / glutamate metabolic process / synaptic transmission, GABAergic / post-embryonic development / central nervous system development / mitochondrial matrix ...Degradation of GABA / succinate-semialdehyde dehydrogenase (NAD+) / succinate-semialdehyde dehydrogenase (NAD+) activity / succinate metabolic process / gamma-aminobutyric acid catabolic process / glutamate metabolic process / synaptic transmission, GABAergic / post-embryonic development / central nervous system development / mitochondrial matrix / synapse / mitochondrion / identical protein binding / cytosol
Similarity search - Function
Succinate semialdehyde dehydrogenase / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain ...Succinate semialdehyde dehydrogenase / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Succinate-semialdehyde dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKim, Y.-G. / Kim, K.-J.
CitationJournal: Embo J. / Year: 2009
Title: Redox-Switch Modulation of Human Ssadh by Dynamic Catalytic Loop.
Authors: Kim, Y.-G. / Lee, S. / Kwon, O.-S. / Park, S.-Y. / Lee, S.-J. / Park, B.-J. / Kim, K.-J.
History
DepositionJan 19, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 9, 2009Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2013Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2Dec 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 / 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 / _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: SUCCINATE-SEMIALDEHYDE DEHYDROGENASE, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0599
Polymers52,2911
Non-polymers7698
Water5,386299
1
A: SUCCINATE-SEMIALDEHYDE DEHYDROGENASE, MITOCHONDRIAL
hetero molecules

A: SUCCINATE-SEMIALDEHYDE DEHYDROGENASE, MITOCHONDRIAL
hetero molecules

A: SUCCINATE-SEMIALDEHYDE DEHYDROGENASE, MITOCHONDRIAL
hetero molecules

A: SUCCINATE-SEMIALDEHYDE DEHYDROGENASE, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,23736
Polymers209,1634
Non-polymers3,07432
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation43_544-x,-z-1/2,-y-1/21
crystal symmetry operation28_544x,-y-1/2,-z-1/21
crystal symmetry operation18_555-x,z,y1
Buried area17880 Å2
ΔGint-82.2 kcal/mol
Surface area61560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)265.706, 265.706, 265.706
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11A-2021-

HOH

-
Components

#1: Protein SUCCINATE-SEMIALDEHYDE DEHYDROGENASE, MITOCHONDRIAL / NAD(+)-DEPENDENT SUCCINIC SEMIALDEHYDE DEHYDROGENASE / ALDEHYDE DEHYDROGENASE FAMILY 5 MEMBER A1 / ...NAD(+)-DEPENDENT SUCCINIC SEMIALDEHYDE DEHYDROGENASE / ALDEHYDE DEHYDROGENASE FAMILY 5 MEMBER A1 / SUCCINIC SEMIALDEHYDE DEHYDROGENASE


Mass: 52290.648 Da / Num. of mol.: 1 / Fragment: RESIDUES 49-535
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PQE30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15(PREP4)
References: UniProt: P51649, succinate-semialdehyde dehydrogenase (NAD+)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.52 Å3/Da / Density % sol: 64.78 % / Description: NONE
Crystal growpH: 7.25 / Details: 100 MM HEPES, PH 7.25, 1.9 M LITHIUM SULFATE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1.2398
DetectorType: ADSC CCD / Detector: CCD / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2398 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 54484 / % possible obs: 96.6 % / Observed criterion σ(I): 0 / Redundancy: 10.2 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.7
Reflection shellHighest resolution: 2 Å / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.4 / % possible all: 92.1

-
Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OPX

2opx


Resolution: 2→30 Å / Data cutoff low absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.25 2659 4.9 %RANDOM
Rwork0.227 ---
obs0.227 52624 96.6 %-
Solvent computationBsol: 37.24 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3627 0 40 299 3966
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.25
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellHighest resolution: 2 Å / Total num. of bins used: 50
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

+
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