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- PDB-8qmr: Succinic semialdehyde dehydrogenase from E. coli with bound NAD+ ... -

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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 / L-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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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Experimental details

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Experiment

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

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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.

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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

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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

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