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- PDB-9nug: D-Ornithine/D-lysine decarboxylase C387A complexed with putrescin... -

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Basic information

Entry
Database: PDB / ID: 9nug
TitleD-Ornithine/D-lysine decarboxylase C387A complexed with putrescine, D-arginine and agmatine
ComponentsD-ornithine/D-lysine decarboxylase
KeywordsLYASE / Decarboxylase / pyridoxal-5'-phosphate / fold III
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
Chem-5DK / : / : / 1,4-DIAMINOBUTANE / D-ornithine/D-lysine decarboxylase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.98 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)2R01GM137008 United States
CitationJournal: To Be Published
Title: D-Ornithine/D-lysine decarboxylase C387A complexed with putrescine and D-arginine
Authors: Phillips, R.S. / Blankenship, S.
History
DepositionMar 19, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 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)110,32814
Polymers108,2882
Non-polymers2,04012
Water12,502694
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10590 Å2
ΔGint-25 kcal/mol
Surface area30150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.025, 49.087, 139.365
Angle α, β, γ (deg.)90.00, 115.88, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-747-

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: 54144.078 Da / Num. of mol.: 2 / Mutation: C387A
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, 706 molecules

#2: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-5DK / (E)-N~2~-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-D-arginine / PLP-DArg


Mass: 403.328 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H22N5O7P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-A1B68 / [(4R)-4-{(E)-[(4-carbamimidamidobutyl)imino]methyl}-6-methyl-5-oxo-4,5-dihydropyridin-3-yl]methyl dihydrogen phosphate


Mass: 359.318 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H22N5O5P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-K / POTASSIUM ION


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-PUT / 1,4-DIAMINOBUTANE / PUTRESCINE


Mass: 88.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12N2 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 694 / 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: 38.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES, pH 7.5, 20% PEG 3350, 0.2-0.4 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.54187 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Sep 11, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 1.98→62.69 Å / Num. obs: 48691 / % possible obs: 80.93 % / Redundancy: 3.1 % / CC1/2: 0.991 / Net I/σ(I): 4.3
Reflection shellResolution: 1.98→2.02 Å / Num. unique obs: 818 / CC1/2: 0.629

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
autoPROCdata processing
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→62.69 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2416 2511 5.16 %
Rwork0.1913 --
obs0.1939 48691 80.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.98→62.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7442 0 127 694 8263
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048114
X-RAY DIFFRACTIONf_angle_d0.65311040
X-RAY DIFFRACTIONf_dihedral_angle_d12.1013083
X-RAY DIFFRACTIONf_chiral_restr0.0471189
X-RAY DIFFRACTIONf_plane_restr0.0061455
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.020.4553450.3764818X-RAY DIFFRACTION26
2.02-2.060.3461680.34641100X-RAY DIFFRACTION36
2.06-2.110.3812630.30321425X-RAY DIFFRACTION45
2.11-2.160.3127930.27671708X-RAY DIFFRACTION54
2.16-2.210.35951270.28662049X-RAY DIFFRACTION65
2.21-2.270.28571500.23442546X-RAY DIFFRACTION82
2.27-2.340.29021710.23872745X-RAY DIFFRACTION88
2.34-2.410.28781480.23782881X-RAY DIFFRACTION92
2.41-2.50.26521560.21672898X-RAY DIFFRACTION92
2.5-2.60.30051540.21442947X-RAY DIFFRACTION93
2.6-2.720.27741650.21392969X-RAY DIFFRACTION95
2.72-2.860.26911730.20783031X-RAY DIFFRACTION95
2.86-3.040.22541510.19783102X-RAY DIFFRACTION98
3.04-3.270.2621510.18513167X-RAY DIFFRACTION98
3.27-3.60.22061610.16353130X-RAY DIFFRACTION99
3.6-4.120.1961750.14273180X-RAY DIFFRACTION99
4.12-5.190.19191510.13723202X-RAY DIFFRACTION99
5.19-62.690.19472090.18843282X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.82920.0677-1.11870.5186-0.51711.57080.001-0.5061-0.11180.0697-0.0847-0.01880.06540.29970.07680.166-0.0225-0.01610.28060.01830.158438.6913-11.491945.5844
22.0933-1.2843-0.4231.51430.02182.06450.20040.4438-0.0963-0.2882-0.21420.02590.14860.03660.01170.19180.0374-0.00390.2933-0.00470.187741.8938-10.635815.7264
31.9859-0.1856-0.87150.4242-0.09051.73150.0003-0.1893-0.24910.006-0.0640.01760.09920.04420.03250.1424-0.0116-0.01370.11430.02550.172128.9063-17.773441.6788
40.55870.4894-0.23871.41810.36193.88430.1614-0.10120.5836-0.2060.01070.1324-0.3515-0.402-0.22240.25270.04880.08930.1894-0.00620.342318.7475.031935.6844
50.69660.2020.20790.2975-0.02880.10030.00140.7067-0.1352-0.42380.01730.11770.1452-0.45610.07680.36260.0004-0.01760.9641-0.03210.19386.7371-11.4446.8167
62.48380.0786-0.58410.8142-0.25181.80620.065-0.0363-0.04120.08210.00270.11730.0147-0.2486-0.04750.14650.01770.0040.219-0.03440.1882-2.2463-10.165442.4484
70.7160.3529-0.27030.6624-0.14941.4877-0.07820.3697-0.273-0.0887-0.03060.00290.2452-0.18260.14460.20870.0084-0.00330.2752-0.09590.20945.8451-18.730224.155
80.92360.1896-0.26370.86160.24211.76140.04340.64190.0565-0.09750.0453-0.05010.0133-0.102-0.11340.17780.03670.01910.4348-0.03250.182717.6143-8.489518.6252
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 93 )
2X-RAY DIFFRACTION2chain 'A' and (resid 94 through 247 )
3X-RAY DIFFRACTION3chain 'A' and (resid 248 through 446 )
4X-RAY DIFFRACTION4chain 'A' and (resid 447 through 467 )
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 47 )
6X-RAY DIFFRACTION6chain 'B' and (resid 48 through 247 )
7X-RAY DIFFRACTION7chain 'B' and (resid 248 through 354 )
8X-RAY DIFFRACTION8chain 'B' and (resid 355 through 466 )

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