[English] 日本語
Yorodumi
- PDB-8qmr: Succinic semialdehyde dehydrogenase from E. coli with bound NAD+ ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8qmr
TitleSuccinic semialdehyde dehydrogenase from E. coli with bound NAD+ and succinic semialdehyde
ComponentsSuccinate semialdehyde dehydrogenase [NAD(P)+] Sad
KeywordsOXIDOREDUCTASE / succinic semialdehyde / dehydrogenase
Function / homology
Function and homology information


succinate-semialdehyde dehydrogenase [NAD(P)+] activity / succinate-semialdehyde dehydrogenase (NADP+) activity / succinate-semialdehyde dehydrogenase [NAD(P)+] / putrescine catabolic process / succinate-semialdehyde dehydrogenase (NAD+) activity / cellular detoxification of nitrogen compound / gamma-aminobutyric acid catabolic process / aldehyde dehydrogenase [NAD(P)+] activity / arginine catabolic process / protein homodimerization activity
Similarity search - Function
Succinate-semialdehyde dehydrogenase GabD1-like / : / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 4-oxobutanoic acid / Succinate semialdehyde dehydrogenase [NAD(P)+] Sad
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHe, H. / Zarzycki, J. / Erb, T.J.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Nat Commun / Year: 2024
Title: Adaptive laboratory evolution recruits the promiscuity of succinate semialdehyde dehydrogenase to repair different metabolic deficiencies.
Authors: He, H. / Gomez-Coronado, P.A. / Zarzycki, J. / Barthel, S. / Kahnt, J. / Claus, P. / Klein, M. / Klose, M. / de Crecy-Lagard, V. / Schindler, D. / Paczia, N. / Glatter, T. / Erb, T.J.
History
DepositionSep 25, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_entry_details / pdbx_modification_feature
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Succinate semialdehyde dehydrogenase [NAD(P)+] Sad
B: Succinate semialdehyde dehydrogenase [NAD(P)+] Sad
C: Succinate semialdehyde dehydrogenase [NAD(P)+] Sad
D: Succinate semialdehyde dehydrogenase [NAD(P)+] Sad
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,14112
Polymers199,0794
Non-polymers3,0628
Water8,305461
1
A: Succinate semialdehyde dehydrogenase [NAD(P)+] Sad
B: Succinate semialdehyde dehydrogenase [NAD(P)+] Sad
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,0706
Polymers99,5392
Non-polymers1,5314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7780 Å2
ΔGint-31 kcal/mol
Surface area31080 Å2
MethodPISA
2
C: Succinate semialdehyde dehydrogenase [NAD(P)+] Sad
D: Succinate semialdehyde dehydrogenase [NAD(P)+] Sad
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,0706
Polymers99,5392
Non-polymers1,5314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7760 Å2
ΔGint-29 kcal/mol
Surface area31130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.520, 115.620, 179.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Succinate semialdehyde dehydrogenase [NAD(P)+] Sad / SSADH / SSDH


Mass: 49769.688 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: sad, yneI, b1525, JW5247 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P76149, succinate-semialdehyde dehydrogenase [NAD(P)+]
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical
ChemComp-SSN / 4-oxobutanoic acid / Succinic semialdehyde


Mass: 102.089 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 461 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.47 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 7.3 mg/mL of SAD in 20 mM HEPES-KOH, 50 mM KCl, pH 7.5 was pre-mixed with NAD+ (final concentration 5 mM). The pre-mixed protein was then mixed in a 2:1 ratio with 250 mM Bis-Tris-Propane, ...Details: 7.3 mg/mL of SAD in 20 mM HEPES-KOH, 50 mM KCl, pH 7.5 was pre-mixed with NAD+ (final concentration 5 mM). The pre-mixed protein was then mixed in a 2:1 ratio with 250 mM Bis-Tris-Propane, pH 8.25, 20 % (w/v) PEG4000. The final drop size was 3 uL. The crystal was soaked with 5 mM succinic semialdehyde for 2 minutes and the drop was complemented with PEG200 to a final concentration of 20 % (v/v) before flash freezing the crystal in liquid nitrogen.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: May 18, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.3→38.07 Å / Num. obs: 85212 / % possible obs: 99.9 % / Redundancy: 8.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.154 / Rrim(I) all: 0.164 / Net I/σ(I): 9.59
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.3-2.360.99862320.8591.0631
2.36-2.420.87760790.9050.9341
2.42-2.490.7458920.9160.7891
2.49-2.570.65357390.9350.6971
2.57-2.660.51355530.9480.551
2.66-2.750.40653830.9570.4391
2.75-2.850.31952470.9760.3441
2.85-2.970.29350310.9870.311
2.97-3.10.23148180.9920.2451
3.1-3.250.18646130.9940.1961
3.25-3.430.14944130.9950.1581
3.43-3.640.11541520.9970.1211
3.64-3.890.10539440.9970.1111
3.89-4.20.09236750.9980.0981
4.2-4.60.0733940.9980.0741
4.6-5.140.07230680.9980.0771
5.14-5.940.08127350.9980.0861
5.94-7.270.07423470.9980.0791
7.27-10.290.0518460.9990.0541
10.29-38.070.05110510.9990.0551

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XSCALEdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→38.07 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2278 1995 2.35 %
Rwork0.1962 --
obs0.197 85024 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→38.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13904 0 204 461 14569
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00314384
X-RAY DIFFRACTIONf_angle_d0.5419520
X-RAY DIFFRACTIONf_dihedral_angle_d11.9685180
X-RAY DIFFRACTIONf_chiral_restr0.0412164
X-RAY DIFFRACTIONf_plane_restr0.0042564
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.28011400.25925842X-RAY DIFFRACTION100
2.36-2.420.2781410.25335882X-RAY DIFFRACTION100
2.42-2.490.26591410.23495849X-RAY DIFFRACTION100
2.49-2.570.27231400.23455860X-RAY DIFFRACTION100
2.57-2.660.29761410.22015859X-RAY DIFFRACTION100
2.66-2.770.27081420.23065898X-RAY DIFFRACTION100
2.77-2.90.25681430.23615889X-RAY DIFFRACTION100
2.9-3.050.28331420.22475892X-RAY DIFFRACTION100
3.05-3.240.2471420.22015895X-RAY DIFFRACTION100
3.24-3.490.23561430.20615937X-RAY DIFFRACTION100
3.49-3.840.20591430.1825935X-RAY DIFFRACTION100
3.84-4.40.20351420.16516000X-RAY DIFFRACTION100
4.4-5.540.18111460.15476041X-RAY DIFFRACTION100
5.54-38.070.17691490.15986250X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 68.181 Å / Origin y: 29.394 Å / Origin z: 59.5086 Å
111213212223313233
T0.3336 Å2-0.001 Å2-0.0057 Å2-0.2693 Å20.0052 Å2--0.2489 Å2
L0.0307 °2-0.0045 °2-0.0007 °2-0.2293 °20.0646 °2--0.1059 °2
S-0.0061 Å °0.0073 Å °-0.0028 Å °0.0098 Å °0.008 Å °0.0142 Å °-0.0008 Å °0.0204 Å °-0.0016 Å °
Refinement TLS groupSelection details: all

+
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