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

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Basic information

Entry
Database: PDB / ID: 9cya
TitleC387S variant of D-ornithine/D-lysine decarboxylase complexed with HEPES and putrescine
ComponentsD-ornithine/D-lysine decarboxylase
KeywordsLYASE / pyridoxal-5'-phosphate / Fold III / decarboxylase / D-amino acid
Function / homology
Function and homology information


D-ornithine/D-lysine decarboxylase / diaminopimelate decarboxylase activity / 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 / 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: 1.4 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
Citation
Journal: To Be Published
Title: Structure of C387S variant of D-ornithine/D-lysine decarboxylase complexed with HEPES and putrescine
Authors: Phillips, R.S. / Blankenship, S.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionAug 1, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,26313
Polymers54,3881
Non-polymers87512
Water8,809489
1
A: D-ornithine/D-lysine decarboxylase
hetero molecules

A: D-ornithine/D-lysine decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,52626
Polymers108,7762
Non-polymers1,75024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area14020 Å2
ΔGint-71 kcal/mol
Surface area30390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.387, 50.591, 73.308
Angle α, β, γ (deg.)90.000, 120.876, 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-507-

ACT

21A-968-

HOH

31A-1003-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 54388.195 Da / Num. of mol.: 1 / 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 , 9 types, 501 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: 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
#5: 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 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#6: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#8: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 489 / 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: 39.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 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: NSLS-II / Beamline: 19-ID / Wavelength: 0.979493 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Oct 18, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979493 Å / Relative weight: 1
ReflectionResolution: 1.4→59.82 Å / Num. obs: 84295 / % possible obs: 98.1 % / Redundancy: 2.9 % / Biso Wilson estimate: 16.2 Å2 / CC1/2: 0.987 / Net I/σ(I): 4.7
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3597 / CC1/2: 0.352 / % possible all: 84.4

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→59.82 Å / SU ML: 0.1697 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.371
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1816 4232 5.04 %
Rwork0.1527 79683 -
obs0.1542 83915 97.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.87 Å2
Refinement stepCycle: LAST / Resolution: 1.4→59.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3685 0 51 491 4227
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00794123
X-RAY DIFFRACTIONf_angle_d1.00345612
X-RAY DIFFRACTIONf_chiral_restr0.081601
X-RAY DIFFRACTIONf_plane_restr0.01739
X-RAY DIFFRACTIONf_dihedral_angle_d13.10761571
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.29451140.30632096X-RAY DIFFRACTION78.15
1.42-1.440.33561180.30362293X-RAY DIFFRACTION84.72
1.44-1.450.33091380.28792475X-RAY DIFFRACTION91.01
1.45-1.470.34811290.26862497X-RAY DIFFRACTION92.89
1.47-1.490.25811450.2612571X-RAY DIFFRACTION95.13
1.49-1.510.27691390.24842661X-RAY DIFFRACTION98.18
1.51-1.530.25141230.23722713X-RAY DIFFRACTION98.85
1.53-1.560.25371260.22842654X-RAY DIFFRACTION99.5
1.56-1.580.21531280.21452734X-RAY DIFFRACTION99.34
1.58-1.610.28551360.20412692X-RAY DIFFRACTION99.51
1.61-1.630.22991710.19732683X-RAY DIFFRACTION99.41
1.63-1.660.25331170.17842712X-RAY DIFFRACTION99.47
1.66-1.690.21981460.17112679X-RAY DIFFRACTION99.44
1.69-1.730.19771470.15922689X-RAY DIFFRACTION99.47
1.73-1.770.20211710.16062676X-RAY DIFFRACTION99.55
1.77-1.810.18421480.15952733X-RAY DIFFRACTION99.62
1.81-1.850.19531340.15972690X-RAY DIFFRACTION99.47
1.85-1.90.20921450.16252685X-RAY DIFFRACTION99.68
1.9-1.960.17171540.15112707X-RAY DIFFRACTION99.76
1.96-2.020.17011230.14082744X-RAY DIFFRACTION99.62
2.02-2.10.16471360.13422714X-RAY DIFFRACTION99.72
2.1-2.180.15731600.1342705X-RAY DIFFRACTION99.9
2.18-2.280.16471310.13112735X-RAY DIFFRACTION100
2.28-2.40.16441390.1282746X-RAY DIFFRACTION99.86
2.4-2.550.1721690.12772687X-RAY DIFFRACTION99.69
2.55-2.750.15721410.13392705X-RAY DIFFRACTION99.51
2.75-3.020.15541630.13622721X-RAY DIFFRACTION99.45
3.02-3.460.16951500.13292723X-RAY DIFFRACTION99.31
3.46-4.360.14261500.12792753X-RAY DIFFRACTION99.35
4.36-59.820.1841410.15762810X-RAY DIFFRACTION98.76
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)
10.3997325913020.06698591774680.1546212505610.188081434135-0.04011481153960.8403831714360.0776074135021-0.647941993795-0.1594082517420.0666685309115-0.04974502904370.1513221851260.0878584191021-0.481351719209-0.1333506927590.192321367414-0.03721762000670.04018370183620.6003633067450.06257927645350.171809781609-16.4722787653-5.3588745478922.0987620845
22.27754001837-0.004741439939530.6158816261220.199815161077-0.09262506393031.37033224284-0.072451769271-0.1856386147150.1096689948820.033264145479-0.0108645839741-0.0458065565033-0.1493005884980.0297769265050.04772461522540.184123732767-0.02279048601880.008136103398240.0950551119257-0.003661882369870.12289056017416.16916932543.2045928709315.9145309727
33.66076743612-1.444292969980.2734738545582.11778172717-0.145705948894.905842333770.1420639049020.475483163837-0.487437978269-0.115077545209-0.0523989933079-0.2238723284820.3704836114630.633510493276-0.1126411570770.2119287424970.07208840227140.03408873488160.215467617221-0.00786192692380.17426312146230.5229641162-10.67646271098.64101678912
42.505133293290.1845257437750.5290997965230.452734203852-0.2679001682691.038391778570.183229265585-0.291066516323-0.4229273609760.0754474819957-0.005231150898950.01550819823310.156887376838-0.0375424083487-0.01437193448280.191844152285-0.032268596197-0.0164919456040.1376393572330.06974142921520.19606657724418.1844788954-11.559046880621.41693971
52.729084178150.3235107768870.464755674910.426839942214-0.08720315508010.8151039783040.068385792132-0.171074029179-0.386842671212-0.07753662317090.06777981081820.01951789606850.132310038709-0.417124144846-0.1122743892760.182321430784-0.04315419680340.01194581061020.2413795335430.06162665528970.183390435908-18.3316841497-9.933573443964.89640837537
61.114257693640.05907067528810.1112820140270.458775153018-0.05922761629091.077876275280.0288263960325-0.378096014309-0.1318123472520.002273978823560.02489552806140.02062938606370.0137326484534-0.350452736859-0.01481769900090.158485589575-0.01376445865080.02170604542030.2298496927440.04585845305220.142435027827-12.1641416337-5.761777912049.96694527603
73.31236540035-0.199813635368-1.142317531951.700965875471.470456668641.55575811195-0.07421694156710.165637716190.417620816267-0.1975354794420.07476223183910.113749880464-0.221155406038-0.1487312772680.0283339851740.2322488204850.0133725869619-0.05276502307620.0576777965384-0.000361644418090.230319624072-4.8779776999914.2755106353-1.71943942208
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 183 )48 - 18348 - 175
33chain 'A' and (resid 184 through 206 )184 - 206176 - 198
44chain 'A' and (resid 207 through 309 )207 - 309199 - 301
55chain 'A' and (resid 310 through 354 )310 - 354302 - 346
66chain 'A' and (resid 355 through 446 )355 - 446347 - 438
77chain 'A' and (resid 447 through 469 )447 - 469439 - 461

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