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- PDB-8d2y: Y430F mutant of D-ornithine/D-lysine decarboxylase -

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Basic information

Entry
Database: PDB / ID: 8d2y
TitleY430F mutant of D-ornithine/D-lysine decarboxylase
ComponentsD-ornithine/D-lysine decarboxylase
KeywordsLYASE / pyridoxal-5'-phosphate / decarboxylase / D-amino acid / 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
ACETATE ION / : / D-ornithine/D-lysine decarboxylase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 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
DepositionMay 31, 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
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,24913
Polymers54,2751
Non-polymers97412
Water11,818656
1
A: D-ornithine/D-lysine decarboxylase
hetero molecules

A: D-ornithine/D-lysine decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,49826
Polymers108,5502
Non-polymers1,94724
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area14350 Å2
ΔGint-30 kcal/mol
Surface area31030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.740, 50.740, 73.320
Angle α, β, γ (deg.)90.000, 120.800, 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-644-

HOH

21A-885-

HOH

31A-1024-

HOH

41A-1111-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 54275.102 Da / Num. of mol.: 1 / Mutation: Y430F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / 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, 668 molecules

#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


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


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 656 / 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: 42.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES, pH 7.5, 0.2-0.4 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: Feb 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.22→36.66 Å / Num. obs: 101867 / % possible obs: 77.91 % / Redundancy: 13.8 % / Biso Wilson estimate: 14.75 Å2 / CC1/2: 0.999 / CC star: 1 / Net I/σ(I): 17.78
Reflection shellResolution: 1.22→1.265 Å / Num. unique obs: 628 / CC1/2: 0.58

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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

6n2h


Resolution: 1.22→36.66 Å / SU ML: 0.1016 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.1929
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1518 2002 1.97 %
Rwork0.1341 99765 -
obs0.1344 101767 77.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.22 Å2
Refinement stepCycle: LAST / Resolution: 1.22→36.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3683 0 57 658 4398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00784280
X-RAY DIFFRACTIONf_angle_d1.14535851
X-RAY DIFFRACTIONf_chiral_restr0.0875620
X-RAY DIFFRACTIONf_plane_restr0.0132778
X-RAY DIFFRACTIONf_dihedral_angle_d13.71821677
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.22-1.250.318660.3767291X-RAY DIFFRACTION3.2
1.25-1.290.3047180.2853932X-RAY DIFFRACTION10.3
1.29-1.320.3375590.31692741X-RAY DIFFRACTION30.15
1.32-1.370.30211170.28195839X-RAY DIFFRACTION64.02
1.37-1.420.24741570.23377864X-RAY DIFFRACTION86.07
1.42-1.470.22551770.19678694X-RAY DIFFRACTION96.16
1.47-1.540.18561820.16199120X-RAY DIFFRACTION99.42
1.54-1.620.16721810.14539100X-RAY DIFFRACTION99.91
1.62-1.720.19841880.14529121X-RAY DIFFRACTION99.94
1.72-1.850.16491810.13629140X-RAY DIFFRACTION99.99
1.85-2.040.1471840.12929162X-RAY DIFFRACTION99.99
2.04-2.340.16451760.12039174X-RAY DIFFRACTION99.96
2.34-2.940.13561880.12089202X-RAY DIFFRACTION100
2.94-36.660.12021880.11719385X-RAY DIFFRACTION99.93
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)
10.788209117176-0.1429241846740.2373567863750.500850584479-0.07304696855860.640358517401-0.00137663915849-0.499543346392-0.05652621434770.06506911124360.009737156988310.0478834243788-0.000856021498993-0.260262796259-0.03305080836890.114840634181-0.02496512382060.01340960002670.3303040834460.03175256059170.0831541966201-4.70367817169-5.1982936552222.9774501845
22.37822520954-0.1909830360340.1813373782530.606792729174-0.1107980035321.73918302298-0.02696321274870.005924787308820.06524253434230.0186292348674-0.0323974719913-0.0425645382135-0.1095191200390.1259761505980.0245832639480.0972616060325-0.0362840972467-0.007164924192750.1151697457330.008481311159540.076944882052122.36948612931.4806602568410.738893692
34.21225541364-1.152007366210.7844129677871.49149659411-0.596983867342.570177400690.1850757894290.262722844376-0.385002111849-0.151990936053-0.110304412241-0.1335116295120.2507445471690.291995819175-0.09546466363120.1448130554580.04183396286110.02566882652780.2093529899680.007942983648510.15501318468630.9063766809-13.60490731638.60393168392
43.009338284250.222918292270.5584934833560.787714046647-0.3289239053861.299278352560.146614213851-0.173866467278-0.3730210654910.0724570996684-0.0580327367759-0.01974889146350.1061299823510.0470840082565-0.06684676027730.104137200132-0.0088278352427-0.01513555218960.1629739092240.02769179918340.11548897419725.4571653733-13.628851261218.6437205467
51.066555485630.281723392198-0.4431383300250.719928299563-0.3624282809550.660474274430.242742237834-0.482639102512-0.6305186881350.0749564735474-0.0846027736523-0.03177635072760.150269355239-0.153159244485-0.08442048946810.141973527944-0.0492353885396-0.04746539552010.211262278190.1221877621970.2385508529656.85042472931-17.84641570820.5876628142
61.140883853780.07054891120740.3254690061870.154092903692-0.03061437644960.5157869647360.0597917356738-0.216588526241-0.185900536870.01172178873270.001325258374060.02090873387560.045373571284-0.154455776072-0.05786215330190.109848995231-0.02013137067190.001362097192460.1800944604560.03478747323990.120776031126-8.93879144074-10.932565702411.2527810779
72.710300971570.224555872331-1.591989600091.193197284691.346802388052.920973113240.02882839523120.1494062422850.29096584586-0.1458732621430.07559578392440.067553082478-0.205852733467-0.0335630172046-0.09017711412690.1454335009930.0173138765336-0.01721589401380.1015255705310.0073239152110.14851235438-4.6011648293411.0077261755-0.841578482775
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 94 )1 - 941 - 94
22chain 'A' and (resid 95 through 183 )95 - 18395 - 176
33chain 'A' and (resid 184 through 206 )184 - 206177 - 199
44chain 'A' and (resid 207 through 247 )207 - 247200 - 240
55chain 'A' and (resid 248 through 283 )248 - 283241 - 276
66chain 'A' and (resid 284 through 446 )284 - 446277 - 439
77chain 'A' and (resid 447 through 468 )447 - 468440 - 461

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