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- PDB-2tod: ORNITHINE DECARBOXYLASE FROM TRYPANOSOMA BRUCEI K69A MUTANT IN CO... -

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Basic information

Entry
Database: PDB / ID: 2tod
TitleORNITHINE DECARBOXYLASE FROM TRYPANOSOMA BRUCEI K69A MUTANT IN COMPLEX WITH ALPHA-DIFLUOROMETHYLORNITHINE
ComponentsPROTEIN (ORNITHINE DECARBOXYLASE)
KeywordsLYASE / POLYAMINE METABOLISM / PYRIDOXAL 5'-PHOSPHATE / ALPHA-BETA BARREL
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
ALPHA-DIFLUOROMETHYLORNITHINE / PYRIDOXAL-5'-PHOSPHATE / Ornithine decarboxylase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGrishin, N.V. / Osterman, A.L. / Brooks, H.B. / Phillips, M.A. / Goldsmith, E.J.
CitationJournal: Biochemistry / Year: 1999
Title: X-ray structure of ornithine decarboxylase from Trypanosoma brucei: the native structure and the structure in complex with alpha-difluoromethylornithine.
Authors: Grishin, N.V. / Osterman, A.L. / Brooks, H.B. / Phillips, M.A. / Goldsmith, E.J.
History
DepositionMay 18, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Nov 17, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (ORNITHINE DECARBOXYLASE)
B: PROTEIN (ORNITHINE DECARBOXYLASE)
C: PROTEIN (ORNITHINE DECARBOXYLASE)
D: PROTEIN (ORNITHINE DECARBOXYLASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,73512
Polymers188,0174
Non-polymers1,7178
Water15,655869
1
A: PROTEIN (ORNITHINE DECARBOXYLASE)
B: PROTEIN (ORNITHINE DECARBOXYLASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,8676
Polymers94,0092
Non-polymers8594
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6260 Å2
ΔGint-26 kcal/mol
Surface area27950 Å2
MethodPISA, PQS
2
C: PROTEIN (ORNITHINE DECARBOXYLASE)
D: PROTEIN (ORNITHINE DECARBOXYLASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,8676
Polymers94,0092
Non-polymers8594
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6270 Å2
ΔGint-27 kcal/mol
Surface area28000 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)66.800, 154.500, 77.100
Angle α, β, γ (deg.)90.00, 90.58, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.99887, -0.00244, 0.04754), (0.00185, -0.99992, -0.01238), (0.04756, -0.01228, 0.99879)33.77943, 20.98611, -0.63235
2given(0.9989, -0.00262, -0.04671), (0.00338, 0.99986, 0.0161), (0.04666, -0.01624, 0.99878)-0.6761, 56.21986, 38.0341
3given(-0.99991, 0.00465, -0.01254), (-0.00462, -0.99999, -0.00265), (-0.01256, -0.00259, 0.99992)32.97342, 77.36642, 38.89211

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Components

#1: Protein
PROTEIN (ORNITHINE DECARBOXYLASE)


Mass: 47004.359 Da / Num. of mol.: 4 / Mutation: K69A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): B21/DG3 / References: UniProt: P07805, ornithine decarboxylase
#2: Chemical
ChemComp-DMO / ALPHA-DIFLUOROMETHYLORNITHINE


Mass: 182.168 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H12F2N2O2 / Comment: medication*YM
#3: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 869 / 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 Å3/Da / Density % sol: 32 %
Crystal growpH: 7
Details: 16% PEG 3350, 0.2 M SOLIUM ACETATE, 100MM HEPES PH 7.5, 20MG/ML PROTEIN DILUTED TWICE, 16C, pH 7.0
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 16 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Details: Grishin, N.V., (1996) Proteins Struct. Funct. Genet., 24, 272.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 %PEG33501drop
20.1 MTris-HCl1drop
30.2 Mammonium acetate1drop
410 mMdithiothreitol1drop
520 mg/mlprotain1drop

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.908
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.908 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 103282 / % possible obs: 97.6 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.9
Reflection
*PLUS
Num. measured all: 339850
Reflection shell
*PLUS
% possible obs: 61.7 % / Mean I/σ(I) obs: 1.9

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
X-PLORrefinement
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 7ODC

7odc


Resolution: 2→8 Å / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflection
Rfree0.27 -10 %
Rwork0.212 --
obs-101011 96.2 %
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11009 0 88 869 11966
Software
*PLUS
Name: 'REFMAC, X-PLOR, CNS' / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / σ(F): 1 / % reflection Rfree: 10 % / Rfactor obs: 0.212 / Rfactor Rfree: 0.27
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_angle_d0.041

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