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- PDB-9y1p: C387S variant of D-ornithine/D-lysine decarboxylase complexed wit... -

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Basic information

Entry
Database: PDB / ID: 9y1p
TitleC387S variant of D-ornithine/D-lysine decarboxylase complexed with PMP and cadaverine
ComponentsD-ornithine/D-lysine decarboxylase
KeywordsLYASE / pyridoxal-5'-phosphate / Fold III / complex
Function / homology
Function and homology information


D-ornithine/D-lysine decarboxylase / diaminopimelate decarboxylase activity / :
Similarity search - Function
Ornithine/DAP/Arg decarboxylase / Orn/DAP/Arg decarboxylase 2, N-terminal / Pyridoxal-dependent decarboxylase, pyridoxal binding domain / Alanine racemase/group IV decarboxylase, C-terminal / PLP-binding barrel
Similarity search - Domain/homology
: / PENTANE-1,5-DIAMINE / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / D-ornithine/D-lysine decarboxylase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPhillips, R.S. / Blankenship, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM137008 United States
CitationJournal: To Be Published
Title: C387S mutant of D-ornithine/D-lysine decarboxylase with bound PMP and cadaverine
Authors: Phillips, R.S. / Blankenship, S.
History
DepositionAug 29, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D-ornithine/D-lysine decarboxylase
B: D-ornithine/D-lysine decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,68717
Polymers108,3202
Non-polymers1,36715
Water15,691871
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12810 Å2
ΔGint-14 kcal/mol
Surface area29930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.070, 49.500, 139.770
Angle α, β, γ (deg.)90.000, 115.637, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-669-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein D-ornithine/D-lysine decarboxylase / D-Orn/D-Lys decarboxylase / DOKDC


Mass: 54160.078 Da / Num. of mol.: 2 / Mutation: C387S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: dokD, STM2360 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q8ZNC4, D-ornithine/D-lysine decarboxylase

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Non-polymers , 7 types, 886 molecules

#2: Chemical ChemComp-PMP / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE


Mass: 248.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H13N2O5P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-N2P / PENTANE-1,5-DIAMINE


Mass: 102.178 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H14N2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 871 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.05 Å3/Da / Density % sol: 40.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES-K, pH 8, 0.2 M sodium acetate, 22% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 31, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→70.77 Å / Num. obs: 61279 / % possible obs: 87.2 % / Redundancy: 3.1 % / Biso Wilson estimate: 26.8 Å2 / CC1/2: 0.676 / Net I/σ(I): 8.1
Reflection shellResolution: 1.8→1.85 Å / Num. unique obs: 8920 / CC1/2: 0.487

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Processing

Software
NameVersionClassification
PHENIX2.0_5793refinement
autoPROCdata processing
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→59.63 Å / SU ML: 0.3144 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.2144
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2531 2012 2.58 %
Rwork0.2107 75822 -
obs0.2118 77834 95.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.55 Å2
Refinement stepCycle: LAST / Resolution: 1.8→59.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7436 0 78 873 8387
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00298122
X-RAY DIFFRACTIONf_angle_d0.56911050
X-RAY DIFFRACTIONf_chiral_restr0.04491194
X-RAY DIFFRACTIONf_plane_restr0.00491463
X-RAY DIFFRACTIONf_dihedral_angle_d12.81093039
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.44721550.41275601X-RAY DIFFRACTION99.53
1.85-1.890.40011310.39715180X-RAY DIFFRACTION91.57
1.89-1.950.39521200.39484459X-RAY DIFFRACTION78.93
1.95-2.010.31571500.32195624X-RAY DIFFRACTION99.47
2.01-2.090.39181250.30864972X-RAY DIFFRACTION87.83
2.09-2.170.29261540.27225611X-RAY DIFFRACTION99.79
2.17-2.270.31231410.26885176X-RAY DIFFRACTION91.19
2.27-2.390.28831500.24395638X-RAY DIFFRACTION99.79
2.39-2.540.30151410.2325667X-RAY DIFFRACTION99.83
2.54-2.730.31131480.22275355X-RAY DIFFRACTION94.13
2.73-3.010.24661440.2025678X-RAY DIFFRACTION99.64
3.01-3.440.21281490.17135561X-RAY DIFFRACTION97.36
3.44-4.340.18941460.14535462X-RAY DIFFRACTION95.1
4.34-59.630.1971580.16085838X-RAY DIFFRACTION98.8

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