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- PDB-9eaf: Carboxyspermidine decarboxylase from Clostridium leptum -

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Basic information

Entry
Database: PDB / ID: 9eaf
TitleCarboxyspermidine decarboxylase from Clostridium leptum
Components
  • Carboxynorspermidine decarboxylase
  • HIS-HIS-HIS-SER-SER-GLY-LEU-VAL
KeywordsBIOSYNTHETIC PROTEIN / spermidine / decarboxylase / pyridoxal 5-phosphate / polyamine biosynthesis / bacterial
Function / homology
Function and homology information


nor-spermidine biosynthetic process / diaminopimelate decarboxylase activity / spermidine biosynthetic process / lysine biosynthetic process via diaminopimelate
Similarity search - Function
Carboxynorspermidine decarboxylase / Orn/DAP/Arg decarboxylase 2, C-terminal / Pyridoxal-dependent decarboxylase, C-terminal sheet domain / Alanine racemase/group IV decarboxylase, C-terminal / PLP-binding barrel
Similarity search - Domain/homology
: / PHOSPHATE ION / Carboxynorspermidine decarboxylase
Similarity search - Component
Biological species[Clostridium] leptum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å
AuthorsJones, S.J. / Bell, D.J. / McFarlane, J.S.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R16GM146714 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RL5GM118990 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T34GM140909 United States
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2025
Title: Structure of Clostridium leptum carboxyspermidine decarboxylase and comparison to homologs prevalent within the human gut microbiome.
Authors: Jones, S.J. / Bell, D.J. / McFarlane, J.S.
History
DepositionNov 10, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carboxynorspermidine decarboxylase
B: Carboxynorspermidine decarboxylase
C: HIS-HIS-HIS-SER-SER-GLY-LEU-VAL
D: HIS-HIS-HIS-SER-SER-GLY-LEU-VAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,57811
Polymers85,0364
Non-polymers5427
Water10,431579
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11180 Å2
ΔGint-68 kcal/mol
Surface area24810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.570, 80.850, 140.535
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

#1: Protein Carboxynorspermidine decarboxylase


Mass: 41642.285 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) [Clostridium] leptum (bacteria) / Gene: nspC, CH238_05290, CLOLEP_01503 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A7VSG2
#2: Protein/peptide HIS-HIS-HIS-SER-SER-GLY-LEU-VAL


Mass: 875.952 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) [Clostridium] leptum (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 4 types, 586 molecules

#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 579 / Source method: isolated from a natural source / Formula: H2O

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Details

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 Å3/Da / Density % sol: 42.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.8 / Details: potassium phosphate dibasic, PEG 8000, glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 19, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.41→38.85 Å / Num. obs: 133970 / % possible obs: 95.8 % / Redundancy: 13.1 % / Biso Wilson estimate: 10.63 Å2 / CC1/2: 0.999 / Net I/σ(I): 12.9
Reflection shellResolution: 1.41→1.45 Å / Num. unique obs: 6885 / CC1/2: 0.923

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.41→38.85 Å / SU ML: 0.1271 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.8508
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1892 1995 1.49 %
Rwork0.1498 131587 -
obs0.1504 133582 95.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.4 Å2
Refinement stepCycle: LAST / Resolution: 1.41→38.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5796 0 31 579 6406
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00366005
X-RAY DIFFRACTIONf_angle_d0.72958153
X-RAY DIFFRACTIONf_chiral_restr0.0691891
X-RAY DIFFRACTIONf_plane_restr0.00571056
X-RAY DIFFRACTIONf_dihedral_angle_d13.91832197
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.41-1.450.30421040.24976885X-RAY DIFFRACTION70.68
1.45-1.480.24751220.21498006X-RAY DIFFRACTION82.38
1.48-1.530.2431390.18189191X-RAY DIFFRACTION94.2
1.53-1.580.20751470.15279669X-RAY DIFFRACTION99.39
1.58-1.630.17411460.14339702X-RAY DIFFRACTION99.11
1.63-1.70.18851460.13269627X-RAY DIFFRACTION98.91
1.7-1.780.16461470.13439704X-RAY DIFFRACTION98.8
1.78-1.870.19481470.13389645X-RAY DIFFRACTION98.49
1.87-1.990.17341460.12849729X-RAY DIFFRACTION99.22
1.99-2.140.15631500.12949804X-RAY DIFFRACTION99.59
2.14-2.360.16741470.12799777X-RAY DIFFRACTION99.12
2.36-2.70.15751480.13879675X-RAY DIFFRACTION97.77
2.7-3.40.19861510.15069972X-RAY DIFFRACTION99.84
3.4-38.850.2061550.168510201X-RAY DIFFRACTION98.77

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