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- PDB-1njj: Crystal structure determination of T. brucei ornithine decarboxyl... -

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Basic information

Entry
Database: PDB / ID: 1njj
TitleCrystal structure determination of T. brucei ornithine decarboxylase bound to D-ornithine and to G418
Componentsornithine decarboxylase
KeywordsLYASE / ornithine decarboxylase / ODC / PLP / pyridoxal 5'-phosphate / D-ornithine / G418
Function / homology
Function and homology information


ornithine decarboxylase / ornithine decarboxylase activity / polyamine biosynthetic process
Similarity search - Function
Ornithine decarboxylase / Orn/DAP/Arg decarboxylase 2, pyridoxal-phosphate binding site / Orn/DAP/Arg decarboxylases family 2 pyridoxal-P attachment site. / 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 / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Lyase, Ornithine Decarboxylase; Chain A, domain 1 ...Ornithine decarboxylase / Orn/DAP/Arg decarboxylase 2, pyridoxal-phosphate binding site / Orn/DAP/Arg decarboxylases family 2 pyridoxal-P attachment site. / 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 / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Alanine racemase / Alanine racemase/group IV decarboxylase, C-terminal / PLP-binding barrel / TIM Barrel / Alpha-Beta Barrel / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GENETICIN / Chem-ORX / Ornithine decarboxylase
Similarity search - Component
Biological speciesTrypanosoma brucei gambiense (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsJackson, L.K. / Goldsmith, E.J. / Phillips, M.A.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: X-ray Structure Determination of Trypanosoma brucei Ornithine Decarboxylase Bound to D-Ornithine and to G418: INSIGHTS INTO SUBSTRATE BINDING AND ODC CONFORMATIONAL FLEXIBILITY.
Authors: Jackson, L.K. / Goldsmith, E.J. / Phillips, M.A.
History
DepositionDec 31, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Advisory / Experimental preparation / Category: exptl_crystal_grow / pdbx_unobs_or_zero_occ_atoms / Item: _exptl_crystal_grow.temp
Revision 1.4Aug 16, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ornithine decarboxylase
B: ornithine decarboxylase
C: ornithine decarboxylase
D: ornithine decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,54511
Polymers188,6024
Non-polymers2,9437
Water3,729207
1
A: ornithine decarboxylase
B: ornithine decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,0216
Polymers94,3012
Non-polymers1,7204
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4630 Å2
ΔGint-39 kcal/mol
Surface area30130 Å2
MethodPISA
2
C: ornithine decarboxylase
D: ornithine decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,5245
Polymers94,3012
Non-polymers1,2233
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-28 kcal/mol
Surface area30810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.818, 88.540, 150.445
Angle α, β, γ (deg.)90.00, 90.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
ornithine decarboxylase /


Mass: 47150.590 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei gambiense (eukaryote)
Species: Trypanosoma brucei / Strain: gambiense / Plasmid: PODC29 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9TZZ6, ornithine decarboxylase
#2: Chemical ChemComp-GET / GENETICIN / G418 / G418


Mass: 496.552 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H40N4O10 / Comment: antibiotic*YM
#3: Chemical
ChemComp-ORX / N~2~-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-D-ORNITHINE


Mass: 363.303 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H22N3O7P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O

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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: 2.82 Å3/Da / Density % sol: 56.11 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Peg 3350, Hepes, DTT, NaCl, D-ornithine, G418, butyrolactone, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 16K
Crystal grow
*PLUS
pH: 7.2 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
123 mg/mlprotein1drop
210 mMHEPES1droppH7.2
350 mM1dropNaCl
410 mMdithiothreitol1drop
50.5 mMEDTA1drop
60.01 %Brij-201drop
720 %PEG33501reservoir
8100 mMHEPES1reservoirpH8.0
910 mMdithiothreitol1reservoir
1025 mMD-Orn1reservoirpH7.5
11100 mMG4181reservoir
1225 mMD-Orn1drop
13100 mMG418 sulfate1drop

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Data collection

DiffractionMean temperature: 98.5 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 1, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 63372 / % possible obs: 96.7 % / Redundancy: 4 % / Biso Wilson estimate: 52 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 21.8
Reflection shellResolution: 2.45→2.54 Å / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.1 / % possible all: 93.9
Reflection
*PLUS
Num. measured all: 253681
Reflection shell
*PLUS
% possible obs: 93.9 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1f3t with waters, K69, C360 and putrescine removed
Resolution: 2.45→35 Å / σ(F): 2 / σ(I): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.283 4953 -RANDOM
Rwork0.26 ---
all-65652 --
obs-49323 87.6 %-
Displacement parametersBiso mean: 45.1 Å2
Refinement stepCycle: LAST / Resolution: 2.45→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11019 0 198 207 11424
LS refinement shellResolution: 2.45→2.54 Å
RfactorNum. reflection
Rfree0.34 297
Rwork0.293 -
obs-2884
Refinement
*PLUS
Rfactor Rwork: 0.26
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.0087
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.559

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