[English] 日本語
Yorodumi
- PDB-4ogd: Crystal structure of succinic semialdehyde dehydrogenase from Str... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ogd
TitleCrystal structure of succinic semialdehyde dehydrogenase from Streptococcus pyogenes in complex with NADP+ as the cofactor
ComponentsSuccinate-semialdehyde dehydrogenase
KeywordsOXIDOREDUCTASE / SSADH / GabD / Rossmann Fold / Dehydrogenase / NADP Binding
Function / homology
Function and homology information


succinate-semialdehyde dehydrogenase (NADP+) / succinate-semialdehyde dehydrogenase (NADP+) activity / succinate-semialdehyde dehydrogenase (NAD+) activity / aldehyde dehydrogenase [NAD(P)+] activity / nucleotide binding
Similarity search - Function
Succinate-semialdehyde dehydrogenase GabD1-like / : / 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 domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal ...Succinate-semialdehyde dehydrogenase GabD1-like / : / 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 domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Succinic semialdehyde dehydrogenase / :
Similarity search - Component
Biological speciesStreptococcus pyogenes MGAS1882 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsJang, E.H. / Park, S.A. / Chi, Y.M. / Lee, K.S.
CitationJournal: Mol.Cells / Year: 2014
Title: Kinetic and Structural Characterization for Cofactor Preference of Succinic Semialdehyde Dehydrogenase from Streptococcus pyogenes.
Authors: Jang, E.H. / Park, S.A. / Chi, Y.M. / Lee, K.S.
History
DepositionJan 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.2Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Succinate-semialdehyde dehydrogenase
B: Succinate-semialdehyde dehydrogenase


Theoretical massNumber of molelcules
Total (without water)103,7222
Polymers103,7222
Non-polymers00
Water9,494527
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-27 kcal/mol
Surface area31850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.259, 100.281, 105.103
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a dimer in the asymmetric unit.

-
Components

#1: Protein Succinate-semialdehyde dehydrogenase


Mass: 51861.227 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: bacteria
Source: (gene. exp.) Streptococcus pyogenes MGAS1882 (bacteria)
Strain: Streptococcus pyogenes / Gene: gabD, MGAS1882_0809 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: H8HE26, UniProt: A0A0J9X1M8*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 527 / 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: 2.37 Å3/Da / Density % sol: 48.08 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M MES monohydrate and 18-23% (w/v) PEG 4000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Jul 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 1262499 / Num. obs: 128443 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.8 % / Biso Wilson estimate: 12.14 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.058 / Net I/σ(I): 26.3
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 2.5 / Num. unique all: 5681 / Rsym value: 0.352 / % possible all: 88.4

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
CNS1.3refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNS1.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3JZ4

3jz4


Resolution: 1.6→17.97 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.48 / Phase error: 17.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1986 6387 4.98 %RANDOM
Rwork0.1742 ---
obs0.1754 128375 98.48 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.3 Å2
Refinement stepCycle: LAST / Resolution: 1.6→17.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7148 0 0 527 7675
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067306
X-RAY DIFFRACTIONf_angle_d1.0339902
X-RAY DIFFRACTIONf_dihedral_angle_d13.182662
X-RAY DIFFRACTIONf_chiral_restr0.0741086
X-RAY DIFFRACTIONf_plane_restr0.0051288
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.5986-1.61680.2451730.21613421342183
1.6168-1.63580.21262030.20883671367191
1.6358-1.65570.2221970.20043768376892
1.6557-1.67670.22561960.19033949394995
1.6767-1.69870.23442070.18633925392597
1.6987-1.7220.21642100.18084048404899
1.722-1.74650.22082190.17534026402699
1.7465-1.77260.20742130.175840834083100
1.7726-1.80030.22082120.172641254125100
1.8003-1.82970.22022290.167240564056100
1.8297-1.86130.19931930.164340894089100
1.8613-1.89510.18712180.165640954095100
1.8951-1.93150.20192260.161340834083100
1.9315-1.97090.19972040.162140894089100
1.9709-2.01370.18742090.161841334133100
2.0137-2.06040.17822230.16941044104100
2.0604-2.11190.19342260.166440974097100
2.1119-2.16890.20331970.167441414141100
2.1689-2.23260.19712270.16940974097100
2.2326-2.30450.18132080.166841384138100
2.3045-2.38670.19842300.172441094109100
2.3867-2.4820.22082000.175941104110100
2.482-2.59470.1982240.176741424142100
2.5947-2.7310.1962170.185741504150100
2.731-2.90150.18692190.181141424142100
2.9015-3.12440.19742190.191141794179100
3.1244-3.43690.20572110.192941884188100
3.4369-3.92970.21192240.175442004200100
3.9297-4.93390.17232230.1542454245100
4.9339-17.97110.18212300.166243854385100

+
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