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- PDB-8d5r: Structure of Y430F D-ornithine/D-lysine decarboxylase complex wit... -

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Basic information

Entry
Database: PDB / ID: 8d5r
TitleStructure of Y430F D-ornithine/D-lysine decarboxylase complex with D-ornithine
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
ACETATE ION / Chem-ORX / 1,4-DIAMINOBUTANE / D-ornithine/D-lysine decarboxylase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 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 6, 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)109,54117
Polymers108,0942
Non-polymers1,44715
Water15,565864
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: The homodimer is the functionally active unit.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11170 Å2
ΔGint-74 kcal/mol
Surface area31270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.530, 50.200, 140.280
Angle α, β, γ (deg.)90.000, 116.000, 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

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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: 54046.984 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, 879 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-ORX / N~2~-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-D-ORNITHINE


Mass: 363.303 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H22N3O7P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / 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: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 864 / 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: 2.15 Å3/Da / Density % sol: 42.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES, 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: Nov 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.44→37.34 Å / Num. obs: 160330 / % possible obs: 99.85 % / Redundancy: 20 % / Biso Wilson estimate: 20.41 Å2 / CC1/2: 0.998 / Net I/σ(I): 12.7
Reflection shellResolution: 1.44→1.491 Å / Mean I/σ(I) obs: 0.79 / Num. unique obs: 15778 / CC1/2: 0.374

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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: 1.44→37.34 Å / SU ML: 0.1949 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.5844
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1903 2000 1.25 %
Rwork0.1646 158223 -
obs0.165 160223 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.53 Å2
Refinement stepCycle: LAST / Resolution: 1.44→37.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7322 0 87 865 8274
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01038260
X-RAY DIFFRACTIONf_angle_d1.070511271
X-RAY DIFFRACTIONf_chiral_restr0.09861202
X-RAY DIFFRACTIONf_plane_restr0.01011501
X-RAY DIFFRACTIONf_dihedral_angle_d13.17243133
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.44-1.480.41751270.397811111X-RAY DIFFRACTION98.64
1.48-1.520.36051480.335111215X-RAY DIFFRACTION99.9
1.52-1.560.33971510.288611243X-RAY DIFFRACTION99.97
1.56-1.610.25351400.246511220X-RAY DIFFRACTION99.99
1.61-1.670.25491450.219211307X-RAY DIFFRACTION99.97
1.67-1.740.23231400.200211238X-RAY DIFFRACTION99.96
1.74-1.810.23171390.184511291X-RAY DIFFRACTION100
1.81-1.910.22311520.17511244X-RAY DIFFRACTION99.94
1.91-2.030.2141310.164211326X-RAY DIFFRACTION99.93
2.03-2.190.19061500.157911284X-RAY DIFFRACTION99.94
2.19-2.410.19821430.154711355X-RAY DIFFRACTION99.98
2.41-2.750.17321470.155311333X-RAY DIFFRACTION100
2.75-3.470.18051400.153211410X-RAY DIFFRACTION99.98
3.47-37.340.14691470.131711646X-RAY DIFFRACTION99.8
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)
12.19266179684-0.399378787281-0.6099165869730.6454045695050.3454014587681.07819398492-0.120828057444-0.6009257819740.2728603579840.1247651737970.175381938984-0.191972574653-0.004013229495740.3558444194770.08260138646680.1645422882010.0702150819803-0.06862954420010.318792835981-0.0522735222510.19213622540539.1485082469-1.3468045279931.6550329791
27.567729822370.1070464228120.1755015864753.336422940522.111966296761.42543101191-0.1165984758580.458983296161-0.693759565272-0.155454617475-0.03578496960130.1932712650940.345018268121-0.1830688218010.1848928561860.1999131562730.0712625005072-0.05579575014640.232118767839-0.04422376287870.21962241015340.5203438172-14.77836252278.52852368748
32.04062875537-0.168142208689-1.825231146471.0946863685-1.39275086135.84531035965-0.275783634647-0.283340167442-0.2323724743680.1017826839710.155031032609-0.06491994469810.32913298130.1618305088670.1119242268180.1769837643340.0714167026707-0.01823451388920.2570887961420.02571817171690.24280320205945.7007429603-14.510084929324.5707573595
41.65045822174-0.369915825762-0.6902707894850.6172123809230.2135764913150.786751825703-0.202368907711-0.720097368156-0.01180178063660.1885717906440.1690364777460.02398325427910.1188440406620.2469084747060.01852375388720.2507739495610.117519108688-0.0227216575530.3965031328560.023927185580.16115157238724.6627111021-6.3649145767943.0516053474
51.93573958912-0.266389562111-0.885779953140.4745929001180.2586181301571.54413986709-0.02621551642650.39046042217-0.157637911687-0.0121279100357-0.04465420612610.08231403971280.00560138182545-0.2860000692530.06653248079110.1429950904540.0353551333102-0.02340569208470.216835253923-0.0332956733120.207688083741.73607511052-5.6053859704417.0198904963
61.567571181560.613554635984-0.4831864786490.670976487475-0.2809735370492.83510944867-0.0139909344597-0.363566306-0.08647482427340.133390864044-0.02342881139740.03382911030280.1716950765910.05150990327030.00117619846920.2254938895850.09037360381650.01551695433490.289922771489-0.01700050902180.2186808988450.110828153952-1.1285802599548.5468298237
72.05869121752-0.584146511841-2.390229545221.010774298931.971768168655.30929777922-0.26299484068-0.155512457474-0.3975279416030.210445773148-0.004970224131790.1098582038830.463682636942-0.08195199282540.2564219555610.215912546970.04778563411380.04044950254480.2006106860440.02312348582670.292252855806-4.92839290773-14.957891477438.6922705625
81.660921448820.167943565604-0.9280097751580.3163871534180.006948844388521.36483718252-0.1203199764860.0728113440908-0.2767845030160.03035537477560.001973983510750.02223187683310.127949238941-0.01513980944420.1206914285290.1835994538160.0316429789864-0.005403975119910.136286011712-0.02950250621110.23463855022711.4680863932-13.636003466621.501165153
91.65321215219-0.200046356145-0.2048325186241.09726240530.6818419582581.50689331906-0.002220476296710.09156896293360.0143722211629-0.0003011245695010.0155530248048-0.0387468335-0.0320304381890.0259682194171-0.0187277253210.1382788600450.0250171837553-0.007357812760250.1294929067450.002015575627850.16520811544918.8009027968-3.4086320560618.3252520875
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 183 )AA1 - 1831 - 175
22chain 'A' and (resid 184 through 206 )AA184 - 206176 - 198
33chain 'A' and (resid 207 through 283 )AA207 - 283199 - 275
44chain 'A' and (resid 284 through 469 )AA284 - 469276 - 461
55chain 'B' and (resid 1 through 94 )BF1 - 941 - 94
66chain 'B' and (resid 95 through 206 )BF95 - 20695 - 198
77chain 'B' and (resid 207 through 283 )BF207 - 283199 - 275
88chain 'B' and (resid 284 through 368 )BF284 - 368276 - 360
99chain 'B' and (resid 369 through 467 )BF369 - 467361 - 459

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