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- PDB-8d88: Structure of Y430F D-ornithine/D-lysine decarboxylase complex wit... -

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Basic information

Entry
Database: PDB / ID: 8d88
TitleStructure of Y430F D-ornithine/D-lysine decarboxylase complex with D-lysine
ComponentsD-ornithine/D-lysine decarboxylase
KeywordsLYASE / pyridoxal-5'-phosphate / D-amino acid / decarboxylase / Fold III
Function / homology
Function and homology information


D-ornithine/D-lysine decarboxylase / diaminopimelate decarboxylase activity / lysine biosynthetic process via diaminopimelate
Similarity search - Function
Orn/DAP/Arg decarboxylase 2, C-terminal / Pyridoxal-dependent decarboxylase, C-terminal sheet domain / 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 / Chem-R1O / D-ornithine/D-lysine decarboxylase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å
AuthorsPhillips, R.S. / Nguyen Hoang, K.N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM137008 United States
CitationJournal: Arch.Biochem.Biophys. / Year: 2022
Title: The Y430F mutant of Salmonella d-ornithine/d-lysine decarboxylase has altered stereospecificity and a putrescine allosteric activation site.
Authors: Phillips, R.S. / Nguyen Hoang, K.N.
History
DepositionJun 8, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)109,94120
Polymers108,2362
Non-polymers1,70518
Water18,2311012
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: The functional unit is the dimer.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11750 Å2
ΔGint-78 kcal/mol
Surface area31390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.240, 50.490, 139.320
Angle α, β, γ (deg.)90.000, 117.260, 90.000
Int Tables number5
Space group name H-MC121
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
11B-833-

HOH

21B-842-

HOH

31B-1041-

HOH

41B-1110-

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: 54118.062 Da / Num. of mol.: 2 / Mutation: Y430F
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 , 8 types, 1030 molecules

#2: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


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


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-N2P / PENTANE-1,5-DIAMINE


Mass: 102.178 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H14N2
#5: Chemical ChemComp-R1O / N~2~-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-D-lysine


Mass: 377.330 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H24N3O7P
Details: Two structures are present, one is the PLP external aldimine of D-Lys, the other is a gem-diamine of PLP, D-Lys, and Lys-80. The external aldimine has a C=N bond at C4' of PLP. The gem- ...Details: Two structures are present, one is the PLP external aldimine of D-Lys, the other is a gem-diamine of PLP, D-Lys, and Lys-80. The external aldimine has a C=N bond at C4' of PLP. The gem-diamine is tetrahedral at C4' of PLP. It is addition of NZ of Lys-80 to 4' of the external aldimine.
Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Na
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cl
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1012 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.13 Å3/Da / Density % sol: 42.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 H HEPES-K, pH 7.5, 0.2 M NaOAc, 20% 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: Mar 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.41→41.28 Å / Num. obs: 161759 / % possible obs: 95.71 % / Redundancy: 5.7 % / Biso Wilson estimate: 19.54 Å2 / CC1/2: 0.999 / Net I/σ(I): 10.63
Reflection shellResolution: 1.41→1.46 Å / Num. unique obs: 12439 / CC1/2: 0.43

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6N2H.pdb

6n2h


Resolution: 1.41→41.28 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1946 1996 1.24 %
Rwork0.175 159189 -
obs0.1752 161185 95.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 127.53 Å2 / Biso mean: 31.1956 Å2 / Biso min: 15.9 Å2
Refinement stepCycle: final / Resolution: 1.41→41.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7332 0 161 1012 8505
Biso mean--40.28 42.98 -
Num. residues----920
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.41-1.450.4781020.4797836471
1.45-1.480.43971300.4441006385
1.48-1.530.33971350.36041136696
1.53-1.580.33241440.31331152798
1.58-1.630.27671550.27341160398
1.63-1.70.26631440.24261165398
1.7-1.780.28031400.21531169199
1.78-1.870.22271580.19581176199
1.87-1.990.20041470.16971172499
1.99-2.140.19861480.15651180699
2.14-2.360.19851420.15161181799
2.36-2.70.1541520.14811185499
2.7-3.40.18951500.14681193399
3.4-41.280.13931490.13991202798
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)
11.00280.0456-0.62930.2186-0.1731.90710.0056-0.3794-0.00010.0255-0.0143-0.05240.0330.39620.01990.184-0.0068-0.03190.3099-0.0190.207537.322-1.58842.484
22.6916-0.293-0.02210.40470.27022.57940.03840.00410.07940.0173-0.068-0.0365-0.03220.06380.00660.1981-0.0056-0.0030.13260.03350.220339.6140.58213.351
36.79671.2122-2.12983.28870.6353.799-0.250.6414-0.4267-0.36860.12830.02520.396-0.19140.11970.26150.0514-0.05190.1911-0.01520.206740.605-12.5887.92
41.6874-0.1224-1.44180.4236-0.40263.013-0.1717-0.2663-0.14150.0083-0.008-0.07390.26470.35930.2290.19850.05480.00210.22450.04520.230146.811-13.12124.544
50.7816-0.0567-0.16160.3922-0.25971.3782-0.0295-0.1715-0.0193-0.00210.0110.02980.08360.04960.02370.19260.0078-0.02230.2104-0.00950.188619.588-5.38845.286
67.2799-3.20633.86667.03483.51397.39445.2807-3.9483-6.20825.8947-3.4444-1.4136-3.04063.9539-1.8471.07020.09410.11310.46010.11420.75872.29919.34628.923
71.26280.0572-0.53280.4350.26941.90540.00790.25170.0214-0.0258-0.0460.0380.0004-0.34430.03640.18910.0173-0.03750.189-0.0240.19231.296-4.13716.224
82.19470.1537-0.27560.2384-0.16092.55160.0509-0.1778-0.0037-0.0392-0.07610.00220.0007-0.00920.00270.19240.0135-0.01990.1624-0.05920.2051-0.2372.46445.369
91.7043-0.0419-1.28820.48780.33982.2748-0.1196-0.0772-0.23220.0724-0.09290.07870.2615-0.19560.24560.2195-0.02730.00360.201-0.03620.2522-6.868-13.23140.401
101.2120.1257-0.18110.43740.35981.5626-0.02780.035-0.012-0.00240.026-0.07960.04280.11390.03550.18970.0127-0.01790.0755-0.00670.184619.423-5.99716.545
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:112 )A1 - 112
2X-RAY DIFFRACTION2( CHAIN A AND RESID 113:183 )A113 - 183
3X-RAY DIFFRACTION3( CHAIN A AND RESID 184:206 )A184 - 206
4X-RAY DIFFRACTION4( CHAIN A AND RESID 207:309 )A207 - 309
5X-RAY DIFFRACTION5( CHAIN A AND RESID 310:466 )A310 - 466
6X-RAY DIFFRACTION6( CHAIN A AND RESID 478:478 )A478
7X-RAY DIFFRACTION7( CHAIN B AND RESID 1:94 )B1 - 94
8X-RAY DIFFRACTION8( CHAIN B AND RESID 95:183 )B95 - 183
9X-RAY DIFFRACTION9( CHAIN B AND RESID 184:309 )B184 - 309
10X-RAY DIFFRACTION10( CHAIN B AND RESID 310:466 )B310 - 466

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