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- PDB-8d4i: Structure of Y430F D-ornithine/D-lysine decarboxylase complex wit... -

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Basic information

Entry
Database: PDB / ID: 8d4i
TitleStructure of Y430F D-ornithine/D-lysine decarboxylase complex with putrescine
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 / 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: 1.32 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 2, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)109,88418
Polymers108,5502
Non-polymers1,33416
Water21,7261206
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: The homodimer is the asymmetric unit and necessary for activity.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12690 Å2
ΔGint-46 kcal/mol
Surface area30860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.880, 50.440, 139.180
Angle α, β, γ (deg.)90.000, 116.930, 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-687-

HOH

21A-906-

HOH

31A-1027-

HOH

41C-894-

HOH

51C-964-

HOH

61C-1085-

HOH

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Components

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Protein , 1 types, 2 molecules AC

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


Mass: 54275.102 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, 1222 molecules

#2: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE / 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 / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PUT / 1,4-DIAMINOBUTANE / PUTRESCINE / Putrescine


Mass: 88.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12N2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#6: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1206 / 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: 2.1 Å3/Da / Density % sol: 41.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / 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: Jul 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.32→41.36 Å / Num. obs: 197103 / % possible obs: 96.27 % / Redundancy: 9.6 % / Biso Wilson estimate: 14.27 Å2 / CC1/2: 0.999 / Net I/σ(I): 11.63
Reflection shellResolution: 1.32→1.367 Å / Num. unique obs: 15354 / CC1/2: 0.0715

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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: 1.32→41.36 Å / SU ML: 0.1407 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.6195
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1709 2010 1.02 %
Rwork0.1461 195093 -
obs0.1463 197103 96.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.23 Å2
Refinement stepCycle: LAST / Resolution: 1.32→41.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7383 0 76 1211 8670
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00768288
X-RAY DIFFRACTIONf_angle_d1.021411316
X-RAY DIFFRACTIONf_chiral_restr0.08221212
X-RAY DIFFRACTIONf_plane_restr0.01041495
X-RAY DIFFRACTIONf_dihedral_angle_d13.7723194
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.32-1.350.37251090.361810389X-RAY DIFFRACTION72.21
1.35-1.390.38381230.318912204X-RAY DIFFRACTION84.68
1.39-1.430.3021460.269213410X-RAY DIFFRACTION93.33
1.43-1.480.25021450.225414185X-RAY DIFFRACTION98.31
1.48-1.530.21711440.187414428X-RAY DIFFRACTION99.92
1.53-1.590.16271400.16114397X-RAY DIFFRACTION99.97
1.59-1.660.16571550.147214402X-RAY DIFFRACTION99.97
1.66-1.750.1721550.136514395X-RAY DIFFRACTION99.97
1.75-1.860.15021450.133514453X-RAY DIFFRACTION99.91
1.86-20.15331490.129314432X-RAY DIFFRACTION99.9
2-2.210.18121510.125414504X-RAY DIFFRACTION99.91
2.21-2.520.15771450.121914509X-RAY DIFFRACTION99.93
2.52-3.180.15281490.129414573X-RAY DIFFRACTION99.96
3.18-41.360.14581540.132614812X-RAY DIFFRACTION99.59
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)
10.824122858929-0.130804714132-0.5610748360090.3047898120370.05538716142821.09737859046-0.0325536146531-0.1391060489490.03513627151040.00284198165440.000238760309188-0.06970960988690.05981174588360.2117352144390.04399333514270.1016862624950.0122986696334-0.02166305085820.1565335995850.007151318391430.14664164791640.4219008631-6.000047581928.0313043456
20.491770535892-0.0450530306-0.3254780116250.192281928872-0.002367373441010.596814507508-0.0477900527162-0.1654745782470.003873878417830.03784794730930.0231128179171-0.02844330104140.06398096671860.1144912522160.02897662553950.1322190708730.0187417848758-0.02742049543620.159862140143-0.004636496788550.11236754983924.2427470638-6.5184530806642.702385348
32.227396856230.8416757109240.2851807631852.228801985140.1355833163132.1792636705-0.03756584400320.186395371262-0.048253732892-0.1955389856880.0470966835697-0.04903134770790.0712266163725-0.1302253888020.005463945448040.1067714014460.0118949304282-0.01385426957110.157211681872-0.01406990075490.06140389586366.99336739648-9.027798016776.29104179746
41.618372960750.822549644368-1.015394015510.961787412441-0.590472257792.062868152970.01928969784280.1712191261360.0986312140639-0.00503689203016-0.01828945573840.0869778912006-0.0236661085448-0.255846520281-0.002650115999960.08940911631440.0357110979569-0.02591746541810.131163159538-0.0257496987560.0994253557238-4.23219865712-1.8768008124226.1659335858
51.735792834990.6473781724970.3211948357851.85687923988-0.6221859339233.78209457089-0.036356474204-0.04267868216430.159694842426-0.0192759881951-0.02533531722630.00951158093801-0.199457830122-0.1230174573530.06075725761810.101864836470.0262840680449-0.008158257217180.0816098562563-0.02813904530960.09017283755440.7803596918264.89183872438.4822092116
62.637852267410.0967924652828-0.05966827482212.21805004741-0.03849171885412.564492621880.0225275906724-0.099884520867-0.05431688886540.00492541125155-0.03099574618940.00324757084780.05373365383090.02189940857950.01603776790620.1085145156660.00604332967867-0.0128633942050.130562198993-0.03192570387860.0792105259008-0.524847890086-0.48312341737350.5954051383
75.455731835630.234129052818-0.3389841597152.44824708321-1.554752136143.48049147348-0.140600411311-0.371767661887-0.3705701028820.3298355197630.0478963518936-0.04107033316630.355220858550.1663197757650.05377173850860.202533788901-0.021885989431-0.04030078483770.1352957206980.01162671493720.0893774806957-1.33079516157-12.667786970954.3582493881
81.19997525035-0.477765907826-1.443515903010.5544811877350.894169638933.0843062989-0.107409731908-0.00735773298738-0.1552166755730.0339817855616-0.05915947111560.09743038584010.203801832363-0.1309400652830.2055303246550.105303411388-0.0167811695582-0.007089988148590.0978599677815-0.01710070980620.109313450578-5.71366186991-14.514220475738.2602679287
91.072035030710.00987134422424-0.7148186191020.2366953011590.1637976098011.23248683973-0.07613779626020.125158415938-0.173847894134-0.0199863910531-0.0227534284028-0.01167872498120.118380257798-0.05382247805770.1280257602420.1314685496240.00838803318957-0.01606742930780.0921702655421-0.02687272823160.13027847820310.1692693817-13.014613930520.9859783312
100.6974569037750.0177959585187-0.04368832160140.7176571718260.4040390546731.035757695050.0002813295097960.03429112180960.035424813647-0.03137142561720.0117581388758-0.0611569815731-0.03609352205980.0280983097681-0.01287246462340.116007847840.00669535437002-0.009167024171630.1104781754230.001700414856130.10821290584617.6067106517-4.076408126718.2407969689
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 283 )AA1 - 2831 - 277
22chain 'A' and (resid 284 through 468 )AA284 - 468278 - 462
33chain 'C' and (resid 1 through 47 )CJ1 - 471 - 47
44chain 'C' and (resid 48 through 94 )CJ48 - 9448 - 94
55chain 'C' and (resid 95 through 127 )CJ95 - 12795 - 127
66chain 'C' and (resid 128 through 183 )CJ128 - 183128 - 178
77chain 'C' and (resid 184 through 206 )CJ184 - 206179 - 201
88chain 'C' and (resid 207 through 283 )CJ207 - 283202 - 278
99chain 'C' and (resid 284 through 354 )CJ284 - 354279 - 349
1010chain 'C' and (resid 355 through 467 )CJ355 - 467350 - 462

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