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- PDB-8cek: Succinyl-CoA Reductase from Clostridium kluyveri (SucD) with NADPH -

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Basic information

Entry
Database: PDB / ID: 8cek
TitleSuccinyl-CoA Reductase from Clostridium kluyveri (SucD) with NADPH
ComponentsSuccinate-semialdehyde dehydrogenase (acetylating)
KeywordsOXIDOREDUCTASE / SSA / succinic semialdehyde / NADPH / NADP+ / SucD / ssr / succinyl-CoA / mesaconyl-CoA / mesaconyl-C1-CoA / SucD_Ck / CkSucD
Function / homologysuccinate-semialdehyde dehydrogenase (acylating) / oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Succinate-semialdehyde dehydrogenase (acetylating)
Function and homology information
Biological speciesClostridium kluyveri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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

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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)199,0938
Polymers196,1204
Non-polymers2,9744
Water19,2041066
1
A: Succinate-semialdehyde dehydrogenase (acetylating)
B: Succinate-semialdehyde dehydrogenase (acetylating)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,5474
Polymers98,0602
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8440 Å2
ΔGint-21 kcal/mol
Surface area32280 Å2
MethodPISA
2
C: Succinate-semialdehyde dehydrogenase (acetylating)
hetero molecules

C: Succinate-semialdehyde dehydrogenase (acetylating)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,5474
Polymers98,0602
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x,y,-z+11
Buried area8490 Å2
ΔGint-21 kcal/mol
Surface area32300 Å2
MethodPISA
3
D: Succinate-semialdehyde dehydrogenase (acetylating)
hetero molecules

D: Succinate-semialdehyde dehydrogenase (acetylating)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,5474
Polymers98,0602
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
Buried area8580 Å2
ΔGint-20 kcal/mol
Surface area32120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.046, 190.828, 190.907
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
11C-771-

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-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1066 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.23 Å3/Da / Density % sol: 61.87 %
Crystal growTemperature: 288.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 45 % w/v Pentaerythritol Propoxylate (5/4 PO/OH) 100 mM MES; pH 6.5 400 mM Potassium chloride
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: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.04→39.44 Å / Num. obs: 159239 / % possible obs: 98.6 % / Redundancy: 12.8 % / CC1/2: 0.998 / Rpim(I) all: 0.059 / Rrim(I) all: 0.215 / Net I/σ(I): 8.5 / Num. measured all: 2045343
Reflection shellResolution: 2.04→2.15 Å / % possible obs: 90.4 % / Redundancy: 8 % / Num. measured all: 169254 / Num. unique obs: 21156 / CC1/2: 0.329 / Rpim(I) all: 0.966 / Rrim(I) all: 2.931 / Net I/σ(I) obs: 0.6

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Processing

Software
NameVersionClassification
SCALAdata scaling
PHENIX1.20.1-4487refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→29.66 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2219 2004 1.45 %
Rwork0.198 --
obs0.1983 138025 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→29.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13813 0 0 1066 14879
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00414067
X-RAY DIFFRACTIONf_angle_d0.58519064
X-RAY DIFFRACTIONf_dihedral_angle_d12.4075188
X-RAY DIFFRACTIONf_chiral_restr0.0472175
X-RAY DIFFRACTIONf_plane_restr0.0042429
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.20.35211430.29199614X-RAY DIFFRACTION100
2.2-2.260.30281390.28099618X-RAY DIFFRACTION100
2.26-2.330.3151420.26559685X-RAY DIFFRACTION100
2.33-2.410.29361400.24469623X-RAY DIFFRACTION100
2.41-2.490.27811400.24359653X-RAY DIFFRACTION100
2.49-2.590.23481420.23449640X-RAY DIFFRACTION100
2.59-2.710.30361430.2229682X-RAY DIFFRACTION100
2.71-2.850.25281430.21799682X-RAY DIFFRACTION100
2.85-3.030.24491440.21469683X-RAY DIFFRACTION100
3.03-3.260.25471430.20849712X-RAY DIFFRACTION100
3.26-3.590.23411420.18889750X-RAY DIFFRACTION100
3.59-4.110.17531480.16799792X-RAY DIFFRACTION100
4.11-5.170.14731420.15749824X-RAY DIFFRACTION100
5.17-29.660.2071530.179410063X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 14.3316 Å / Origin y: -23.6325 Å / Origin z: 47.3039 Å
111213212223313233
T0.3059 Å20.0249 Å2-0.0192 Å2-0.3057 Å20.009 Å2--0.2877 Å2
L0.0774 °20.0232 °2-0.0283 °2-0.1601 °2-0.008 °2--0.1076 °2
S-0.0044 Å °-0.0081 Å °0.0139 Å °0.0698 Å °0.0035 Å °-0.0465 Å °-0.0024 Å °-0.0615 Å °-0.0006 Å °
Refinement TLS groupSelection details: all

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