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- PDB-9nq5: D-Ornithine/D-lysine decarboxylase C387A complexed with HEPES, pu... -

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Basic information

Entry
Database: PDB / ID: 9nq5
TitleD-Ornithine/D-lysine decarboxylase C387A complexed with HEPES, putrescine, and D-ornithine
Components(D-ornithine/D-lysine ...) x 2
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
: / D-ORNITHINE / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / 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: 1.74 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 HEPES, putrescine, and D-ornithine
Authors: Phillips, R.S. / Blankenship, S.
History
DepositionMar 11, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 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)110,44326
Polymers108,5162
Non-polymers1,92624
Water14,466803
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14140 Å2
ΔGint-73 kcal/mol
Surface area30950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.990, 104.770, 106.260
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

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D-ornithine/D-lysine ... , 2 types, 2 molecules AB

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


Mass: 54372.195 Da / Num. of mol.: 1 / 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
#2: Protein D-ornithine/D-lysine decarboxylase / D-Orn/D-Lys decarboxylase / DOKDC


Mass: 54144.078 Da / Num. of mol.: 1 / 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 , 11 types, 827 molecules

#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-PUT / 1,4-DIAMINOBUTANE / PUTRESCINE


Mass: 88.151 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12N2 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#9: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#10: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#11: Chemical ChemComp-PMP / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE


Mass: 248.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H13N2O5P / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical ChemComp-ORD / D-ORNITHINE


Type: D-peptide linking / Mass: 132.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12N2O2 / Feature type: SUBJECT OF INVESTIGATION
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 803 / 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: 2.31 Å3/Da / Density % sol: 46.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES, pH 7.5, 0.2-0.4 M NaOAc, 20-24% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.978565 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 17, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978565 Å / Relative weight: 1
ReflectionResolution: 1.74→68.67 Å / Num. obs: 103202 / % possible obs: 99.77 % / Redundancy: 6.3 % / CC1/2: 0.998 / Net I/σ(I): 7.22
Reflection shellResolution: 1.74→1.76 Å / Mean I/σ(I) obs: 1.16 / Num. unique obs: 6405 / CC1/2: 0.261

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
autoPROCdata processing
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.74→68.67 Å / SU ML: 0.2712 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.2816
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2068 2002 1.94 %
Rwork0.1791 101187 -
obs0.1797 103189 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47 Å2
Refinement stepCycle: LAST / Resolution: 1.74→68.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7449 0 110 803 8362
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01028167
X-RAY DIFFRACTIONf_angle_d0.832111118
X-RAY DIFFRACTIONf_chiral_restr0.0591192
X-RAY DIFFRACTIONf_plane_restr0.00741471
X-RAY DIFFRACTIONf_dihedral_angle_d13.09233095
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.780.48081400.45547005X-RAY DIFFRACTION98.31
1.78-1.830.41351400.40397184X-RAY DIFFRACTION99.95
1.83-1.890.38421490.35047152X-RAY DIFFRACTION99.97
1.89-1.950.3361370.30067170X-RAY DIFFRACTION99.97
1.95-2.020.28211370.26287181X-RAY DIFFRACTION99.9
2.02-2.10.29811470.23417220X-RAY DIFFRACTION99.95
2.1-2.190.22321430.20477168X-RAY DIFFRACTION99.85
2.19-2.310.23181480.1867199X-RAY DIFFRACTION99.93
2.31-2.450.20311370.17347217X-RAY DIFFRACTION99.92
2.45-2.640.21621430.1667227X-RAY DIFFRACTION99.89
2.64-2.910.22121410.16737254X-RAY DIFFRACTION99.86
2.91-3.330.18041440.15077275X-RAY DIFFRACTION99.81
3.33-4.190.13031470.12557344X-RAY DIFFRACTION99.72
4.19-68.670.16631490.14227591X-RAY DIFFRACTION99.7
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)
12.370231521060.354526180966-0.8553989529040.884993324736-0.373178435081.68797938496-0.004853141147830.1845322596020.1447679928490.1169552828360.1932636932350.3115154034310.041134785717-0.432564686092-0.06450566991020.2070932282110.03704237043210.05540911847770.4032983932620.1219596021570.304312378378-25.44580671423.1679093312-40.8070494457
26.91553936641-0.02036186174532.191058982995.64612235633-3.279015641453.758613485290.5172081195110.552212049119-0.657436715811-0.0236639180814-0.226645561940.3527692982280.486171879101-0.013504752969-0.128777175710.4432006818360.02632437718610.1258377850520.731632212160.07087993680250.374367698543-34.717249077710.7996364346-21.5065355555
32.066691140430.527494137921-0.6493968003441.0738570859-0.4517396488581.46017462492-0.0399709174787-0.128452502556-0.1511125542770.1232392713430.06137795936870.1246917307270.131282446821-0.0932575724792-0.001488127879430.2042020449930.03088545730380.03112181600450.3265522600840.06864474731860.192989282201-15.364107110117.5116342308-38.8056047221
40.250036116917-0.1951141476960.2904919395770.4792463858390.2368064652631.093229432180.0170800110341-0.5288808453210.03291002241160.6459334881920.1413567575940.309688954438-0.2375101708610.052845587114-0.04171055117490.788748393593-0.1185456799730.2668589483391.011101401920.04475613045990.271635714328-12.015378129525.9244342873-0.970660567594
50.0473218768567-0.0334988126130.02493406289770.406385352216-0.293672474810.201305298480.27665675976-0.5414489189620.1462212926220.465123285254-0.203027138418-0.0228436698029-0.2413316098640.3902900507210.02235182969350.472866779595-0.1715896888640.04088380538290.79778420566-0.0473712769010.250609624748.3462918601738.0089530478-24.9440653714
63.67172967171.787185199950.02813247625312.259433698220.4206312420220.3743097295810.300279069975-0.673868336504-0.6268092863370.402542419493-0.421705218014-0.262387253320.09103353841440.3501620663770.13630764560.3429166170480.00928180366219-0.05124728865170.8027255507090.1416987201510.31010914271417.542648356824.7979149747-32.8732479816
70.629909802210.298082701534-0.2106707781720.333854464829-0.07494999712420.07500162481820.0647794247832-0.507186514617-0.3208953498770.257057778677-0.22066588552-0.3252431633750.07893221028320.2927566055610.15630332180.364388154728-0.0651366255876-0.1095839335371.012767261280.2312305683630.32389798000522.29041292225.721320514-26.2695159693
80.05957729068350.004853815542820.08569424547130.2784157189970.1363867342940.1644240934710.0595509658533-0.395604080752-0.3147527579050.540103024757-0.188351981329-0.223141989932-0.1228370620.40429853845-0.2361180540780.498207877672-0.157692851739-0.1652982714661.19128467240.2370414085180.13791876746114.719951683723.6579708377-14.5163186621
91.05181592361.046100950180.3492694571671.87925183535-0.1585699017050.4432099092990.259574436283-0.05772003594260.1538832102520.432422688949-0.03541348841140.346298501627-0.2371689583020.062560803447-0.2165373700180.422165455490.01980643423460.1252662034530.5888170098880.05404662027730.256169650593-20.915058666515.7235255071-13.161470114
100.563330685883-0.70037495722-0.2779893650370.9782172918590.608929145612.479410250770.165712789603-0.5469663948940.05037238753480.395027205157-0.04749523409170.165359280486-0.2067771143780.236564780394-0.1077163097290.466816632407-0.03967143015680.1419671708520.6406412722180.04096298434930.26660901815-14.83559180623.3184112708-13.2092447452
110.7515638732611.831193084311.70062418334.490415537413.978018020426.324458678730.134467893551-0.501685990120.5359404387520.34997735078-0.1487727663430.63729705055-0.385296336362-0.7003969520360.111245257470.4363135649480.08774685042310.2391818623830.5062016299650.01340411689180.476395105608-19.789491236339.8496906168-29.6584415401
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 160 )AA1 - 1601 - 160
22chain 'A' and (resid 161 through 205 )AA161 - 205161 - 205
33chain 'A' and (resid 206 through 466 )AA206 - 466206 - 466
44chain 'B' and (resid 1 through 47 )BB1 - 471 - 47
55chain 'B' and (resid 48 through 160 )BB48 - 16048 - 160
66chain 'B' and (resid 161 through 205 )BB161 - 205161 - 205
77chain 'B' and (resid 206 through 247 )BB206 - 247206 - 247
88chain 'B' and (resid 248 through 309 )BB248 - 309248 - 309
99chain 'B' and (resid 310 through 354 )BB310 - 354310 - 354
1010chain 'B' and (resid 355 through 446 )BB355 - 446355 - 446
1111chain 'B' and (resid 447 through 468 )BB447 - 468447 - 468

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