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- PDB-8cej: Succinyl-CoA Reductase from Clostridium kluyveri (SucD) with Mesa... -

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Basic information

Entry
Database: PDB / ID: 8cej
TitleSuccinyl-CoA Reductase from Clostridium kluyveri (SucD) with Mesaconyl-C1-CoA
ComponentsSuccinate-semialdehyde dehydrogenase (acetylating)
KeywordsOXIDOREDUCTASE / SSA / succinic semialdehyde / NADPH / NADP+ / SucD / ssr / succinyl-CoA / mesaconyl-CoA / mesaconyl-C1-CoA / SucD_Ck / CkSucD / CETCH / Clostridium / succinate / mesaconyl-cystein
Function / homology
Function and homology information


succinate-semialdehyde dehydrogenase (acylating) / oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
Similarity search - Function
Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
(2E)-2-METHYLBUT-2-ENEDIOIC ACID / Mesaconyl Coenzme A / Succinate-semialdehyde dehydrogenase (acetylating)
Similarity search - Component
Biological speciesClostridium kluyveri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPfister, P. / Diehl, C. / Erb, T.J.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Biochemistry / Year: 2023
Title: Enhancing the Substrate Specificity of Clostridium Succinyl-CoA Reductase for Synthetic Biology and Biocatalysis.
Authors: Pfister, P. / Diehl, C. / Hammarlund, E. / Carrillo, M. / Erb, T.J.
History
DepositionFeb 2, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.accession_code / _pdbx_initial_refinement_model.source_name / _pdbx_initial_refinement_model.type
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _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 (acetylating)
B: Succinate-semialdehyde dehydrogenase (acetylating)
C: Succinate-semialdehyde dehydrogenase (acetylating)
D: Succinate-semialdehyde dehydrogenase (acetylating)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,3908
Polymers196,1204
Non-polymers1,2704
Water25,0051388
1
A: Succinate-semialdehyde dehydrogenase (acetylating)
hetero molecules

A: Succinate-semialdehyde dehydrogenase (acetylating)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,3204
Polymers98,0602
Non-polymers2602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-11
Buried area7100 Å2
ΔGint-10 kcal/mol
Surface area32820 Å2
MethodPISA
2
B: Succinate-semialdehyde dehydrogenase (acetylating)
hetero molecules

C: Succinate-semialdehyde dehydrogenase (acetylating)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,0704
Polymers98,0602
Non-polymers1,0102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_344-x-3/2,y-1/2,-z-1/21
Buried area6680 Å2
ΔGint-11 kcal/mol
Surface area32610 Å2
MethodPISA
3
D: Succinate-semialdehyde dehydrogenase (acetylating)
hetero molecules

D: Succinate-semialdehyde dehydrogenase (acetylating)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,3204
Polymers98,0602
Non-polymers2602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z1
Buried area7130 Å2
ΔGint-6 kcal/mol
Surface area32650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.890, 190.650, 190.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-759-

HOH

21A-864-

HOH

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Components

#1: Protein
Succinate-semialdehyde dehydrogenase (acetylating)


Mass: 49029.910 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium kluyveri (bacteria) / Gene: sucD, CKL_3015 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P38947, succinate-semialdehyde dehydrogenase (acylating)
#2: Chemical ChemComp-MEZ / (2E)-2-METHYLBUT-2-ENEDIOIC ACID / MESACONIC ACID / MESACONATE


Mass: 130.099 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H6O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-OA9 / Mesaconyl Coenzme A / (~{E})-4-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethylsulfanyl]-3-methyl-4-oxidanylidene-but-2-enoic acid / Mesaconyl-CoA / 2-methylfumaroyl-CoA


Mass: 879.618 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H40N7O19P3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1388 / 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: 3.25 Å3/Da / Density % sol: 62.18 %
Crystal growTemperature: 288.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM magnesium acetate, 100 mM MOPS pH 7.5, 5 mM mesaconyl-CoA 12% PEG 8000
PH range: 6.5 - 7.8

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.1→25 Å / Num. obs: 149464 / % possible obs: 99.9 % / Redundancy: 2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.115 / Rrim(I) all: 0.125 / Net I/σ(I): 12.21
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.1-2.150.643109760.9270.6951
2.15-2.210.549107270.9430.5931
2.21-2.280.457104140.9590.4941
2.28-2.350.388101030.9670.4211
2.35-2.420.32598320.9720.3541
2.42-2.510.29794600.9770.3231
2.51-2.60.25291700.9840.2721
2.6-2.710.20988520.9880.2261
2.71-2.830.17984710.9880.1941
2.83-2.970.14981270.9910.1621
2.97-3.130.12776980.9910.1391
3.13-3.320.10573300.9930.1141
3.32-3.550.0968930.9950.0971
3.55-3.830.07964300.9960.0851
3.83-4.20.0759010.9960.0761
4.2-4.70.06553580.9960.0721
4.7-5.420.06347970.9970.0691
5.42-6.640.0640320.9970.0651
6.64-9.390.05531730.9970.061
9.39-250.04917200.9980.0541

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
SCALAdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→25 Å / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 37.16 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2422 2014 1.35 %
Rwork0.2113 --
obs0.2218 149464 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13712 0 0 1388 15100
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00213942
X-RAY DIFFRACTIONf_angle_d0.48718867
X-RAY DIFFRACTIONf_dihedral_angle_d10.5955191
X-RAY DIFFRACTIONf_chiral_restr0.0422149
X-RAY DIFFRACTIONf_plane_restr0.0032435
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.27071410.295210465X-RAY DIFFRACTION99
2.15-2.210.32981440.282510460X-RAY DIFFRACTION99
2.21-2.280.29821420.265410442X-RAY DIFFRACTION99
2.28-2.350.25871410.266810453X-RAY DIFFRACTION99
2.35-2.430.28911420.257110438X-RAY DIFFRACTION99
2.43-2.530.27671420.261210495X-RAY DIFFRACTION99
2.53-2.650.26731430.251310482X-RAY DIFFRACTION99
2.65-2.780.27951430.245710496X-RAY DIFFRACTION99
2.78-2.960.24991430.236110500X-RAY DIFFRACTION99
2.96-3.190.27521430.228110531X-RAY DIFFRACTION99
3.19-3.510.25741440.223310538X-RAY DIFFRACTION99
3.51-4.010.23781450.200410615X-RAY DIFFRACTION99
4.01-5.050.21261480.17110634X-RAY DIFFRACTION99
5.05-250.20691500.185610904X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -88.7433 Å / Origin y: -39.9712 Å / Origin z: -47.3632 Å
111213212223313233
T0.1633 Å2-0.0005 Å2-0.0018 Å2-0.1278 Å20.0006 Å2--0.3425 Å2
L0.1409 °20.0153 °20.019 °2-0.0618 °2-0.0074 °2--0.1094 °2
S-0.0051 Å °0.0035 Å °0.0024 Å °0.0156 Å °0.0011 Å °-0.0056 Å °-0.0091 Å °-0.0023 Å °0.0041 Å °
Refinement TLS groupSelection details: all

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