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- PDB-8qmt: Succinic semialdehyde dehydrogenase from E. coli with Q262R subst... -

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Basic information

Entry
Database: PDB / ID: 8qmt
TitleSuccinic semialdehyde dehydrogenase from E. coli with Q262R substitution and bound NAD+, 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: 1.8 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 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Oct 30, 2024Group: Database references / Category: citation / citation_author
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

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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)202,25712
Polymers199,1954
Non-polymers3,0628
Water23,2931293
1
A: Succinate semialdehyde dehydrogenase [NAD(P)+] Sad
B: Succinate semialdehyde dehydrogenase [NAD(P)+] Sad
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,1296
Polymers99,5982
Non-polymers1,5314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7770 Å2
ΔGint-29 kcal/mol
Surface area30910 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)101,1296
Polymers99,5982
Non-polymers1,5314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7580 Å2
ΔGint-32 kcal/mol
Surface area31060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.710, 115.110, 179.380
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: 49798.754 Da / Num. of mol.: 4 / Mutation: Q262R
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.: 1293 / 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: 2.38 Å3/Da / Density % sol: 48.25 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 14.8 mg/mL of SAD_Q262R 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 250 mM Bis-Tris-Propane, pH 7.5 , 20 % (w/v) ...Details: 14.8 mg/mL of SAD_Q262R 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 250 mM Bis-Tris-Propane, pH 7.5 , 20 % (w/v) PEG4000. The final drop size was 3 uL. The drop was complemented with 6 mM succininc semialdehyde and 25 % (v/v) PEG400 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: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 20, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.8→29.55 Å / Num. obs: 174478 / % possible obs: 98.6 % / Redundancy: 13.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.098 / Rrim(I) all: 0.102 / Net I/σ(I): 16.73
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.8-1.841.6126250.8421.6631
1.84-1.891.23124710.9171.2761
1.89-1.950.947121970.9370.9831
1.95-2.010.727115890.9620.7561
2.01-2.070.567113310.9780.5891
2.07-2.150.467111440.9860.4841
2.15-2.230.361107770.9910.3741
2.23-2.320.275103600.9950.2851
2.32-2.420.22899510.9960.2371
2.42-2.540.18695350.9960.1931
2.54-2.680.14590940.9980.1511
2.68-2.840.11484520.9980.1191
2.84-3.040.09178900.9980.0951
3.04-3.280.07576210.9990.0771
3.28-3.590.05869900.9990.061
3.59-4.020.0563580.9990.0521
4.02-4.640.04356190.9990.0451
4.64-5.680.04145670.9990.0431
5.68-8.030.035377110.0371
8.03-29.550.026213610.0271

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XSCALEdata scaling
XDSdata reduction
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→29.55 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2054 1999 1.15 %
Rwork0.1802 --
obs0.1805 174080 98.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→29.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13912 0 204 1294 15410
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00614392
X-RAY DIFFRACTIONf_angle_d0.87119528
X-RAY DIFFRACTIONf_dihedral_angle_d13.1365188
X-RAY DIFFRACTIONf_chiral_restr0.0532164
X-RAY DIFFRACTIONf_plane_restr0.0132564
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.33371390.299512018X-RAY DIFFRACTION97
1.84-1.890.27991420.256312158X-RAY DIFFRACTION98
1.89-1.950.29331420.232312234X-RAY DIFFRACTION99
1.95-2.010.22891400.213312021X-RAY DIFFRACTION97
2.01-2.080.25931410.196512109X-RAY DIFFRACTION98
2.08-2.160.21781430.182812299X-RAY DIFFRACTION99
2.16-2.260.21071420.173412289X-RAY DIFFRACTION99
2.26-2.380.19261440.171412307X-RAY DIFFRACTION99
2.38-2.530.2191430.171712315X-RAY DIFFRACTION99
2.53-2.730.20331430.17312404X-RAY DIFFRACTION99
2.73-30.20781410.177412077X-RAY DIFFRACTION97
3-3.430.16761450.177112512X-RAY DIFFRACTION100
3.43-4.320.18571470.164312614X-RAY DIFFRACTION100
4.32-29.550.19821470.171112724X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -22.4993 Å / Origin y: -29.453 Å / Origin z: -30.2199 Å
111213212223313233
T0.2806 Å2-0.0003 Å20.0029 Å2-0.2466 Å2-0.0092 Å2--0.2281 Å2
L0.0274 °2-0.0032 °20.0042 °2-0.2464 °2-0.0448 °2--0.0365 °2
S0.0014 Å °0.0043 Å °-0.0015 Å °0.0265 Å °0.008 Å °-0.011 Å °-0.0074 Å °-0.0214 Å °-0.0061 Å °
Refinement TLS groupSelection details: all

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