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

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Basic information

Entry
Database: PDB / ID: 8qmq
TitleSuccinic semialdehyde dehydrogenase from E. coli with bound NAD+
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 / Succinate semialdehyde dehydrogenase [NAD(P)+] Sad
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 / pdbx_entry_details
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

Downloads & links

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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)201,7328
Polymers199,0794
Non-polymers2,6544
Water28,8061599
1
A: Succinate semialdehyde dehydrogenase [NAD(P)+] Sad
B: Succinate semialdehyde dehydrogenase [NAD(P)+] Sad
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,8664
Polymers99,5392
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7680 Å2
ΔGint-33 kcal/mol
Surface area31480 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)100,8664
Polymers99,5392
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7750 Å2
ΔGint-31 kcal/mol
Surface area31540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.080, 116.350, 180.070
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1599 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.42 Å3/Da / Density % sol: 49.23 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 33.6 mg/mL of SAD in 20 mM HEPES-KOH, 50 mM KCl, pH 7.5 was complemented with 5 mM NAD+. The enzyme was then mixed in a 2:1 ratio with 285 mM Bis-Tris-Propane, 8.25 pH , 17 % (w/v) PEG4000. ...Details: 33.6 mg/mL of SAD in 20 mM HEPES-KOH, 50 mM KCl, pH 7.5 was complemented with 5 mM NAD+. The enzyme was then mixed in a 2:1 ratio with 285 mM Bis-Tris-Propane, 8.25 pH , 17 % (w/v) PEG4000. The final drop size was 3 uL. The drop was complemented with PEG200 to a final concentration of 20 % (v/v) before flash freezing the crystals in liquid nitrogen.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Mar 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.7→19.92 Å / Num. obs: 211048 / % possible obs: 99.7 % / Redundancy: 13.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.09 / Rrim(I) all: 0.094 / Net I/σ(I): 18.56
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.7-1.750.946152430.9330.9841
1.75-1.790.793151020.9540.8241
1.79-1.850.617147200.9780.6411
1.85-1.90.495142600.9790.5141
1.9-1.960.39138860.9860.4051
1.96-2.030.315133820.9910.3271
2.03-2.110.252129580.9940.2611
2.11-2.20.2124950.9960.2081
2.2-2.290.166119710.9970.1721
2.29-2.410.139114830.9980.1451
2.41-2.540.118109240.9980.1231
2.54-2.690.102103320.9980.1061
2.69-2.880.08397310.9990.0871
2.88-3.110.06991000.9990.0721
3.11-3.40.05683960.9990.0581
3.4-3.80.04776180.9990.0481
3.8-4.390.04675510.0421
4.39-5.380.037573210.0391
5.38-7.610.04452110.0411
7.61-19.920.036243910.0381

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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: 1.7→19.92 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1868 1997 0.95 %
Rwork0.1692 --
obs0.1694 210729 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13904 0 176 1599 15679
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00614398
X-RAY DIFFRACTIONf_angle_d0.79219560
X-RAY DIFFRACTIONf_dihedral_angle_d12.6465196
X-RAY DIFFRACTIONf_chiral_restr0.0522172
X-RAY DIFFRACTIONf_plane_restr0.0072570
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.29191390.218414519X-RAY DIFFRACTION98
1.74-1.790.23531420.209914759X-RAY DIFFRACTION100
1.79-1.840.22971420.198814773X-RAY DIFFRACTION100
1.84-1.90.2531400.185214788X-RAY DIFFRACTION100
1.9-1.970.23961410.178114804X-RAY DIFFRACTION100
1.97-2.050.19861430.173914841X-RAY DIFFRACTION100
2.05-2.140.21031420.161714885X-RAY DIFFRACTION100
2.14-2.260.191420.161214870X-RAY DIFFRACTION100
2.26-2.40.18461420.162214881X-RAY DIFFRACTION100
2.4-2.580.16141430.170614925X-RAY DIFFRACTION100
2.58-2.840.22171440.177714994X-RAY DIFFRACTION100
2.84-3.250.18881430.180915018X-RAY DIFFRACTION100
3.25-4.090.161450.159515141X-RAY DIFFRACTION100
4.09-19.920.15341490.152915534X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -69.5976 Å / Origin y: -29.5229 Å / Origin z: 120.2946 Å
111213212223313233
T0.2731 Å2-0.0038 Å2-0.002 Å2-0.2204 Å2-0.0044 Å2--0.1113 Å2
L0.015 °2-0.0143 °20.0046 °2-0.1811 °2-0.0841 °2--0.1658 °2
S-0.0037 Å °0.0005 Å °0.0009 Å °-0.0049 Å °0.0104 Å °0.0081 Å °0.0009 Å °-0.0033 Å °-0.0052 Å °
Refinement TLS groupSelection details: all

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