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- PDB-1f3t: CRYSTAL STRUCTURE OF TRYPANOSOMA BRUCEI ORNITHINE DECARBOXYLASE (... -

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Basic information

Entry
Database: PDB / ID: 1f3t
TitleCRYSTAL STRUCTURE OF TRYPANOSOMA BRUCEI ORNITHINE DECARBOXYLASE (ODC) COMPLEXED WITH PUTRESCINE, ODC'S REACTION PRODUCT.
ComponentsORNITHINE DECARBOXYLASE
KeywordsLYASE / beta-alpha-barrel / modified Greek key beta-sheet
Function / homology
Function and homology information


ornithine decarboxylase / putrescine biosynthetic process from arginine, via ornithine / ornithine decarboxylase activity / polyamine biosynthetic process / cytoplasm
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 decarboxylases family 2 signature 2. / 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 / 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 decarboxylases family 2 signature 2. / 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 / 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
PYRIDOXAL-5'-PHOSPHATE / 1,4-DIAMINOBUTANE / Ornithine decarboxylase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsJackson, L.K. / Brooks, H.B. / Osterman, A.L. / Goldsmith, E.J. / Phillips, M.A.
CitationJournal: Biochemistry / Year: 2000
Title: Altering the reaction specificity of eukaryotic ornithine decarboxylase.
Authors: Jackson, L.K. / Brooks, H.B. / Osterman, A.L. / Goldsmith, E.J. / Phillips, M.A.
History
DepositionJun 6, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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)189,59112
Polymers188,2504
Non-polymers1,3418
Water6,846380
1
A: ORNITHINE DECARBOXYLASE
B: ORNITHINE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,7966
Polymers94,1252
Non-polymers6714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6160 Å2
ΔGint-19 kcal/mol
Surface area30480 Å2
MethodPISA
2
C: ORNITHINE DECARBOXYLASE
D: ORNITHINE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,7966
Polymers94,1252
Non-polymers6714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6230 Å2
ΔGint-19 kcal/mol
Surface area29020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.294, 151.599, 86.414
Angle α, β, γ (deg.)90.00, 103.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
ORNITHINE DECARBOXYLASE / ODC


Mass: 47062.461 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote)
Description: MODIFIED PET-11D PLASMID WITH HIS6-TAG, TEV PROTEASE SITE AND T7 PROMOTOR. HIS6-TAG WAS CLEAVED.
Production host: Escherichia coli (E. coli) / References: UniProt: P07805, ornithine decarboxylase
#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical
ChemComp-PUT / 1,4-DIAMINOBUTANE / PUTRESCINE


Mass: 88.151 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H12N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 380 / 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: 2.28 Å3/Da / Density % sol: 46.02 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 3350, sodium acetate, HEPES, DTT, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289.0K
Crystal grow
*PLUS
Temperature: 16 ℃ / Details: used microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
125 mg/mlprotein1drop
210 mMHEPES1drop
350 mM1dropNaCl
410 mMdithiothreitol1drop
50.5 mMEDTA1drop
60.01 %Brij-201drop
715 mMD-Orn1drop
820 %PEG33501reservoir
90.2 M1reservoirNaOAc
10100 mMHEPES1reservoir
1110 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 23, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2→8 Å / Num. all: 111660 / Num. obs: 104951 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 29.6 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.9
Reflection shellResolution: 2→8 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.319 / Num. unique all: 10827 / % possible all: 96.8
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 111865 / % possible obs: 99.3 % / Num. measured all: 402763 / Rmerge(I) obs: 0.07
Reflection shell
*PLUS
% possible obs: 96.8 % / Mean I/σ(I) obs: 3.2

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2→8 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.28 2099 -random
Rwork0.237 ---
all-111660 --
obs-104951 99.3 %-
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11737 0 84 380 12201
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0096
X-RAY DIFFRACTIONc_angle_deg1.5
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 8 Å / σ(F): 0 / Rfactor obs: 0.237 / Rfactor Rfree: 0.28
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 29.6 Å2
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.5

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