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- PDB-10li: D-Ornithine/D-lysine decarboxylase complexed with putrescine and ... -

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Basic information

Entry
Database: PDB / ID: 10li
TitleD-Ornithine/D-lysine decarboxylase complexed with putrescine and agmatine
ComponentsDiaminopimelate decarboxylase
KeywordsLYASE / decarboxylase / PLP-dependent / Fold type III
Function / homology
Function and homology information


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
ACETATE ION / AGMATINE / 1,4-DIAMINOBUTANE / Diaminopimelate decarboxylase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.67 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)GM137008 United States
CitationJournal: To Be Published
Title: D-Ornithine/D-lysine decarboxylase complexed with putrescine and agmatine
Authors: Phillips, R.S. / Blankenship, S.
History
DepositionJan 26, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 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: Diaminopimelate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,32916
Polymers54,4041
Non-polymers92415
Water13,385743
1
A: Diaminopimelate decarboxylase
hetero molecules

A: Diaminopimelate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,65732
Polymers108,8092
Non-polymers1,84930
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area15570 Å2
ΔGint-140 kcal/mol
Surface area30140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.413, 50.556, 73.281
Angle α, β, γ (deg.)90.000, 120.692, 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-1074-

HOH

21A-1124-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Diaminopimelate decarboxylase


Mass: 54404.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: lysA_1, A3Y76_06550, AAB27_07220, AU613_21760, AVC05_12620, B1P38_05720, CE70_14345, CFF59_15330, DD95_01965, DMO92_13220, DPF41_09855, DPS76_08380, DRM14_11030, DU071_05960, E0935_14000, EER35_ ...Gene: lysA_1, A3Y76_06550, AAB27_07220, AU613_21760, AVC05_12620, B1P38_05720, CE70_14345, CFF59_15330, DD95_01965, DMO92_13220, DPF41_09855, DPS76_08380, DRM14_11030, DU071_05960, E0935_14000, EER35_06850, F3R12_16115, GB466_10640, SE14_02571
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0D6FAR3

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Non-polymers , 8 types, 758 molecules

#2: 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
#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-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-AG2 / AGMATINE / (4-AMINOBUTYL)GUANIDINE


Mass: 130.191 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H14N4 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 743 / 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: 2.04 Å3/Da / Density % sol: 39.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES, pH 7.5, 0.2 M NaOAc, 22% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.54187 Å
DetectorType: DECTRIS PILATUS 1M / Detector: PIXEL / Date: Dec 30, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 1.572→41.61 Å / Num. obs: 48055 / % possible obs: 78.41 % / Redundancy: 4.2 % / Biso Wilson estimate: 11.22 Å2 / CC1/2: 0.965 / Net I/σ(I): 10.2
Reflection shellResolution: 1.572→1.6 Å / Num. unique obs: 167 / CC1/2: 0.703

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Processing

Software
NameVersionClassification
PHENIX2.0_5936refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.67→36.63 Å / SU ML: 0.1362 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.5603
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1802 2292 4.93 %
Rwork0.1415 44222 -
obs0.1434 46514 90.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.71 Å2
Refinement stepCycle: LAST / Resolution: 1.67→36.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3693 0 51 748 4492
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01114143
X-RAY DIFFRACTIONf_angle_d0.84195624
X-RAY DIFFRACTIONf_chiral_restr0.0509601
X-RAY DIFFRACTIONf_plane_restr0.0083746
X-RAY DIFFRACTIONf_dihedral_angle_d13.39941572
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.67-1.710.2481550.24411262X-RAY DIFFRACTION41.64
1.71-1.750.2613910.21661687X-RAY DIFFRACTION55.91
1.75-1.790.23691270.19552202X-RAY DIFFRACTION73.35
1.79-1.840.24871420.20752734X-RAY DIFFRACTION90.78
1.84-1.890.19561480.16842994X-RAY DIFFRACTION98.71
1.89-1.950.19751490.1832986X-RAY DIFFRACTION98.9
1.95-2.020.23031680.17442972X-RAY DIFFRACTION98.37
2.02-2.10.18151700.13752990X-RAY DIFFRACTION99.18
2.1-2.20.17741500.13212994X-RAY DIFFRACTION99.15
2.2-2.320.16911710.12532988X-RAY DIFFRACTION99.18
2.32-2.460.18491330.13013047X-RAY DIFFRACTION99.25
2.46-2.650.22971390.13293062X-RAY DIFFRACTION99.81
2.65-2.920.14731330.13343042X-RAY DIFFRACTION99.87
2.92-3.340.1651770.12243058X-RAY DIFFRACTION99.97
3.34-4.210.15291470.11123093X-RAY DIFFRACTION99.97
4.21-36.630.14921920.13863111X-RAY DIFFRACTION99.73
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)
10.39521310574689-0.11113470219517-0.0222231184464950.57943012666983-0.196688753191450.883430398871180.075521541802661-0.52541411708313-0.180059007570110.038604201461233-0.028637637801630.206698832094680.082783240543643-0.173280791416960.00797775107479650.061160845491827-0.0368161725753380.0493265251008110.268300170290810.0517174504468520.014136008731001-16.297510144286-7.177413011010122.43439464394
20.92142265152881-0.00196208758084430.205531196851410.221200817130010.000698862510188830.285778437732120.020455522183582-0.230971557348030.11435322509580.041976295962064-0.041112039301189-0.044417930163271-0.069931915599421-0.0202516991359180.0180461057610690.083434045715137-0.017660492614393-0.000686010941907970.096350884248931-0.0180615280933920.04662284897682115.0926874923712.831084202590816.076543976989
32.0150722822479-0.167420965049180.176208237122612.06756683680720.301031340586782.34505005757950.061966469230996-0.035165174768187-0.26579244247146-0.12448595594617-0.12283482267875-0.0787655740100350.206459730638250.155650280239280.0664318968849990.0993022165129740.0101581862780.0208968555584990.0707839607913040.0345510328992730.07947723868881228.603785596064-9.95273688419929.9565741739443
41.0376693566754-0.29204238636840.120854042110010.64327589967704-0.24102193591890.931368074260170.051475691000628-0.23612446070148-0.235333155184260.054934101972709-0.0429673376622090.00920471232314170.11377093798736-0.0137672043359430.0357265323276550.10052655152112-0.028519603858717-0.0138579765860290.118851284235930.0477820940393010.09910177350446224.476309071892-12.59200256016418.647411557716
50.734803859222-0.12475246214696-0.146263425242730.11411032257195-0.0418207829616090.230453471677250.088837838282067-0.39129722952555-0.208943854051740.016198777715821-0.0434555271547860.0126783373127170.10331210367299-0.1242540514739-0.0701487977219470.11221123704921-0.046777550637208-0.00842925338261680.0815729807204840.0833218859824870.10085719807046-0.24628108203282-13.09063063727615.768680634068
60.87360039510680.0423658888011470.0601146006786410.48201166563191-0.101481627691770.604213168810760.027058178610967-0.13689915652311-0.011886114544988-0.0016499827303852-0.0148183789553390.015064211620915-0.0040727658535475-0.0781873609291-0.00888456807651390.052994237626145-0.00436451915321620.00947221308260760.0489939859099760.00126236187698420.039473907397344-10.654451797258-2.83184843184897.6313666677785
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 47 )1 - 471 - 47
22chain 'A' and (resid 48 through 160 )48 - 16048 - 160
33chain 'A' and (resid 161 through 206 )161 - 206161 - 200
44chain 'A' and (resid 207 through 247 )207 - 247201 - 241
55chain 'A' and (resid 248 through 354 )248 - 354242 - 348
66chain 'A' and (resid 355 through 466 )355 - 466349 - 460

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