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- PDB-8cei: Succinyl-CoA Reductase from Clostridium kluyveri (SucD) -

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Basic information

Entry
Database: PDB / ID: 8cei
TitleSuccinyl-CoA Reductase from Clostridium kluyveri (SucD)
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 / Succinate-semialdehyde dehydrogenase (acetylating)
Function and homology information
Biological speciesClostridium kluyveri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / refine
Item: _pdbx_initial_refinement_model.type / _refine.pdbx_starting_model

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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)


Theoretical massNumber of molelcules
Total (without water)196,1204
Polymers196,1204
Non-polymers00
Water18,4471024
1
A: Succinate-semialdehyde dehydrogenase (acetylating)
B: Succinate-semialdehyde dehydrogenase (acetylating)


Theoretical massNumber of molelcules
Total (without water)98,0602
Polymers98,0602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6460 Å2
ΔGint-17 kcal/mol
Surface area32510 Å2
MethodPISA
2
C: Succinate-semialdehyde dehydrogenase (acetylating)
D: Succinate-semialdehyde dehydrogenase (acetylating)


Theoretical massNumber of molelcules
Total (without water)98,0602
Polymers98,0602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6440 Å2
ΔGint-15 kcal/mol
Surface area32680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.231, 89.339, 137.322
Angle α, β, γ (deg.)90.00, 104.64, 90.00
Int Tables number4
Space group name H-MP1211

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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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1024 / Source method: isolated from a natural source / Formula: H2O

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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: 2.61 Å3/Da / Density % sol: 52.86 %
Crystal growTemperature: 288.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25 % w/v Pentaerythritol Propoxylate (5/4 PO/OH) 100 mM MES; pH 6.5 50 mM Magnesium chloride
PH range: 6.5-7.8

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Data collection

DiffractionMean temperature: 80 K / Ambient temp details: cryostream / 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: 2.2→39.47 Å / Num. obs: 197254 / % possible obs: 99.2 % / Redundancy: 4.4 % / CC1/2: 0.995 / Rpim(I) all: 0.054 / Rrim(I) all: 0.116 / Net I/σ(I): 7.3
Reflection shellResolution: 2.2→2.32 Å / % possible obs: 96 % / Redundancy: 4.4 % / Num. measured all: 62718 / Num. unique obs: 14359 / CC1/2: 0.945 / Rpim(I) all: 0.22 / Rrim(I) all: 0.468 / Net I/σ(I) obs: 2.7

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K9D

3k9d


Resolution: 2.2→39.47 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 33.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.267 3860 1.96 %
Rwork0.2424 --
obs0.2429 197254 97.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→39.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13576 0 0 1024 14600
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00113804
X-RAY DIFFRACTIONf_angle_d0.39218668
X-RAY DIFFRACTIONf_dihedral_angle_d9.8865144
X-RAY DIFFRACTIONf_chiral_restr0.0422132
X-RAY DIFFRACTIONf_plane_restr0.0032408
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.220.34281150.31195694X-RAY DIFFRACTION80
2.22-2.250.29981230.29636969X-RAY DIFFRACTION99
2.25-2.280.28751410.28757060X-RAY DIFFRACTION99
2.28-2.310.29181410.29186891X-RAY DIFFRACTION98
2.31-2.350.31271410.28637035X-RAY DIFFRACTION99
2.35-2.380.36191470.29276927X-RAY DIFFRACTION99
2.38-2.420.33011540.27936939X-RAY DIFFRACTION98
2.42-2.460.33741360.27536998X-RAY DIFFRACTION98
2.46-2.50.30731180.26716866X-RAY DIFFRACTION98
2.5-2.540.29831460.26536958X-RAY DIFFRACTION97
2.54-2.590.24581310.24586799X-RAY DIFFRACTION96
2.59-2.650.27511540.26446903X-RAY DIFFRACTION98
2.65-2.70.30871360.26116979X-RAY DIFFRACTION98
2.7-2.770.31521520.2516955X-RAY DIFFRACTION99
2.77-2.840.30561230.25486939X-RAY DIFFRACTION98
2.84-2.910.21871360.21877050X-RAY DIFFRACTION99
2.91-30.28291410.27076963X-RAY DIFFRACTION99
3-3.10.31551420.25627064X-RAY DIFFRACTION99
3.1-3.210.26681470.25176956X-RAY DIFFRACTION99
3.21-3.330.32021310.24526771X-RAY DIFFRACTION96
3.33-3.490.22641400.22646877X-RAY DIFFRACTION97
3.49-3.670.28431380.22487050X-RAY DIFFRACTION99
3.67-3.90.25611340.2167087X-RAY DIFFRACTION99
3.9-4.20.23831510.20766955X-RAY DIFFRACTION99
4.2-4.620.20611240.20436988X-RAY DIFFRACTION99
4.62-5.290.1961430.1966861X-RAY DIFFRACTION97
5.29-6.660.28611330.23547051X-RAY DIFFRACTION100
6.66-100.22391420.20296809X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 1.1918 Å / Origin y: -0.932 Å / Origin z: 89.664 Å
111213212223313233
T0.201 Å2-0.0072 Å2-0.0219 Å2-0.2114 Å2-0.0133 Å2--0.2194 Å2
L0.0641 °2-0.024 °20.1482 °2-0.069 °2-0.0761 °2--0.1055 °2
S-0.0016 Å °0.0017 Å °-0.0017 Å °0.0112 Å °-0.0084 Å °-0.0134 Å °-0.008 Å °0.0078 Å °0.0083 Å °
Refinement TLS groupSelection details: all

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