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- PDB-9cpz: C387S variant of D-ornithine/D-lysine decarboxylase complexed wit... -

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Basic information

Entry
Database: PDB / ID: 9cpz
TitleC387S variant of D-ornithine/D-lysine decarboxylase complexed with PMP and 4-guanidinobutanal
ComponentsD-ornithine/D-lysine decarboxylase
KeywordsLYASE / pyridoxal-5'-phosphate / decarboxylase / aminotransferase fold
Function / homology
Function and homology information


D-ornithine/D-lysine decarboxylase / diaminopimelate decarboxylase activity / L-lysine biosynthetic process via diaminopimelate
Similarity search - Function
Ornithine/DAP/Arg decarboxylase / Orn/DAP/Arg decarboxylase 2, C-terminal / Pyridoxal-dependent decarboxylase, C-terminal sheet domain / 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 / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / D-ornithine/D-lysine decarboxylase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 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)R01 GM137008 United States
CitationJournal: To Be Published
Title: Structure of C387S DOKDC soaked with D-Arg
Authors: Phillips, R.S. / Blankenship, S.
History
DepositionJul 18, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2025Provider: 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)109,52814
Polymers108,3202
Non-polymers1,20812
Water16,051891
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12050 Å2
ΔGint-55 kcal/mol
Surface area29810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.590, 49.110, 139.810
Angle α, β, γ (deg.)90.000, 115.803, 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: 54160.078 Da / Num. of mol.: 2 / Mutation: C387S
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 , 7 types, 903 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-NA / SODIUM ION


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


Mass: 248.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H13N2O5P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-A1AZK / N-(4-oxobutyl)guanidine


Mass: 129.160 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11N3O / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-ACT / ACETATE ION


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 891 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.02 Å3/Da / Density % sol: 39.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M HEPES-K, pH 7.5, 0.2-0.4 M sodium acetate, 20% PEG 3350

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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: Apr 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.54→48.92 Å / Num. obs: 83046 / % possible obs: 92.5 % / Redundancy: 6.7 % / Biso Wilson estimate: 22.39 Å2 / CC1/2: 0.995 / Net I/σ(I): 7.8
Reflection shellResolution: 1.54→1.71 Å / Num. unique obs: 4154 / CC1/2: 0.528

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.54→48.92 Å / SU ML: 0.1954 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.9739
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2132 2004 2.41 %
Rwork0.1676 81042 -
obs0.1687 83046 64.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.23 Å2
Refinement stepCycle: LAST / Resolution: 1.54→48.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7433 0 73 893 8399
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00648099
X-RAY DIFFRACTIONf_angle_d0.831511022
X-RAY DIFFRACTIONf_chiral_restr0.05211188
X-RAY DIFFRACTIONf_plane_restr0.00721463
X-RAY DIFFRACTIONf_dihedral_angle_d13.39573066
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.580.248950.261301X-RAY DIFFRACTION3.38
1.58-1.620.2961180.2742734X-RAY DIFFRACTION8.26
1.62-1.670.2601290.29321251X-RAY DIFFRACTION14.04
1.67-1.720.309590.28012301X-RAY DIFFRACTION26.01
1.72-1.780.3139950.28583778X-RAY DIFFRACTION42.25
1.78-1.860.27051300.26355119X-RAY DIFFRACTION57.54
1.86-1.940.2871540.2486316X-RAY DIFFRACTION71.02
1.94-2.040.25061810.22347491X-RAY DIFFRACTION83.27
2.04-2.170.27832150.20298695X-RAY DIFFRACTION97.91
2.17-2.340.26352220.19119006X-RAY DIFFRACTION99.91
2.34-2.570.22462290.18158911X-RAY DIFFRACTION99.74
2.57-2.950.23712190.17178964X-RAY DIFFRACTION99.92
2.95-3.710.17682270.14219006X-RAY DIFFRACTION99.6
3.71-48.920.17112210.12939169X-RAY DIFFRACTION98.88
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)
10.502213592753-0.1192660641150.1097406911370.503840155275-0.1284981539910.375486717571-0.200809393177-0.9228807760770.1493753536630.7643761261430.203032292794-0.1940937448220.02087020571530.3906103851250.3857544677120.2428694567210.227997602006-0.2356256546230.581356337289-0.0679863056293-0.039159898017739.0441387953-2.7305110085945.2259986647
22.42991715653-0.716126048874-0.09565810702191.905206080320.6041530311152.28692388684-0.02368319241810.147105106220.01872977152590.02508053127860.094124294968-0.06721661629650.1060164652740.177566180099-0.05237913750220.08119132522860.0136827644159-0.009360733030890.1527661873310.02264900792260.11292803116239.5493911107-3.4716650408215.0199311067
31.49437187483-0.359012137816-0.1332098676610.9633328156010.2382232426850.641888247773-0.203762024648-0.464198704001-0.01856225979670.3242567065110.199596574088-0.05714414029050.127108510150.193855447222-0.002094424871740.233237455030.145432137058-0.03149679836030.2213258556060.03787931998550.060522397763731.0321426801-8.1126904183537.6695871311
41.47930267041-0.314501373791-0.5856487943970.7467209572460.2531838295031.42107000403-0.01900009975520.437202517061-0.1956798777130.0108072031617-0.1374679634170.1905879255490.0320680226357-0.3125168926470.1580841502830.1238846605530.0298995969508-0.0025432139290.195579919902-0.06241359822510.2067419384221.53144977454-5.5555696467616.9236145541
51.586651367740.337870711137-0.1148436225450.7805203125040.3680314694131.12138971448-0.130985197828-0.363904621688-0.222566729930.265262186153-0.02222700241530.140680338670.3725188543640.08125517609370.08240863149590.3500697759420.08814721447570.129080090330.2177449711120.01644370498930.236178556504-1.54661435513-4.5041101803647.0017755386
60.2234917394360.2913720759560.02417489879850.5342148284030.0978580645851.04992563305-0.1828313725340.0777070414051-0.5002532853560.154922951977-0.05426803481920.1223035036320.238129428816-0.04452053279020.1082020376940.1916317232740.04336264069960.08810905471460.0666088754187-0.02452893926460.3240524324736.77250858435-14.614055849925.0564369489
71.77248467369-0.134955491481-0.06845413909381.189608306270.5044222917561.29348124201-0.04135181332350.155842214127-0.0393762581790.05870951830530.001268762624780.0387579502977-0.01672786501120.03197821688860.01767794625850.09568828920850.0379431025860.01129581429620.09949104931460.00419412543020.10507070301917.879035007-4.8190459826618.762875077
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 94 )AA2 - 942 - 94
22chain 'A' and (resid 95 through 206 )AA95 - 20695 - 206
33chain 'A' and (resid 207 through 480 )AA207 - 480207 - 470
44chain 'B' and (resid 2 through 94 )BB2 - 941 - 93
55chain 'B' and (resid 95 through 247 )BB95 - 24794 - 246
66chain 'B' and (resid 248 through 354 )BB248 - 354247 - 353
77chain 'B' and (resid 355 through 466 )BB355 - 466354 - 465

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