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- PDB-7odc: CRYSTAL STRUCTURE ORNITHINE DECARBOXYLASE FROM MOUSE, TRUNCATED 3... -

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Entry
Database: PDB / ID: 7odc
TitleCRYSTAL STRUCTURE ORNITHINE DECARBOXYLASE FROM MOUSE, TRUNCATED 37 RESIDUES FROM THE C-TERMINUS, TO 1.6 ANGSTROM RESOLUTION
ComponentsPROTEIN (ORNITHINE DECARBOXYLASE)
KeywordsLYASE / PYRIDOXAL-5'-PHOSPHATE / PLP / GROUP IV DECARBOXYLASE / POLYAMINES / PARASITICAL / CHEMOTHERAPY TARGET / ORNITHINE / PUTRESCINE / A/B-BARREL / OBLIGATE
Function / homology
Function and homology information


Metabolism of polyamines / putrescine biosynthetic process / Regulation of ornithine decarboxylase (ODC) / ornithine decarboxylase / putrescine biosynthetic process from arginine, via ornithine / ornithine decarboxylase activity / polyamine metabolic process / regulation of protein catabolic process / kidney development / response to virus ...Metabolism of polyamines / putrescine biosynthetic process / Regulation of ornithine decarboxylase (ODC) / ornithine decarboxylase / putrescine biosynthetic process from arginine, via ornithine / ornithine decarboxylase activity / polyamine metabolic process / regulation of protein catabolic process / kidney development / response to virus / cell population proliferation / positive regulation of cell population proliferation / perinuclear region of cytoplasm / protein homodimerization activity / cytoplasm / cytosol
Similarity search - Function
Ornithine decarboxylase / Orn/DAP/Arg decarboxylase 2, conserved site / 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 ...Ornithine decarboxylase / Orn/DAP/Arg decarboxylase 2, conserved site / 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 / Ornithine decarboxylase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.6 Å
AuthorsKern, A.D. / Oliveira, M.A. / Coffino, P. / Hackert, M.L.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: Structure of mammalian ornithine decarboxylase at 1.6 A resolution: stereochemical implications of PLP-dependent amino acid decarboxylases.
Authors: Kern, A.D. / Oliveira, M.A. / Coffino, P. / Hackert, M.L.
History
DepositionMar 3, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Oct 22, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / 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_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

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Assembly

Deposited unit
A: PROTEIN (ORNITHINE DECARBOXYLASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5232
Polymers47,2761
Non-polymers2471
Water7,584421
1
A: PROTEIN (ORNITHINE DECARBOXYLASE)
hetero molecules

A: PROTEIN (ORNITHINE DECARBOXYLASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,0464
Polymers94,5522
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area5610 Å2
ΔGint-22 kcal/mol
Surface area31060 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)118.500, 74.000, 45.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein PROTEIN (ORNITHINE DECARBOXYLASE) / ODC / MODC / MODC'


Mass: 47275.801 Da / Num. of mol.: 1 / Mutation: TRUNCATED AFTER RESIDUE 424
Source method: isolated from a genetically manipulated source
Details: SCHIFF-BASE LINKAGE BETWEEN PLP AND K69 / Source: (gene. exp.) Mus musculus (house mouse) / Tissue: LYMPHOMA
Description: THE GENE WAS CLONED FROM A BALB-C MOUSE LYMPHOMA CELL LINE IN WHICH THE ODC GENE WAS AMPLIFIED BY SELECTION WITH DFMO. THE CELL LINE OF ORIGIN WAS S49.1, OBTAINED FROM THE SALK INSTITUTE ...Description: THE GENE WAS CLONED FROM A BALB-C MOUSE LYMPHOMA CELL LINE IN WHICH THE ODC GENE WAS AMPLIFIED BY SELECTION WITH DFMO. THE CELL LINE OF ORIGIN WAS S49.1, OBTAINED FROM THE SALK INSTITUTE CELL CULTURE CENTER IN 1974. THE ODC- AMPLIFIED LYMPHOMA CELL LINE OBTAINED AS A RESULT OF SELECTION WITH DFMO WAS D4. THE GENE HAS BEEN CLONED FROM MANY MOUSE STRAINS SINCE, AND THE ORF IS INVARIANT AMONG THESE, SO FAR AS WE KNOW. THE EXPRESSION OF THE PROTEIN WAS IN E.COLI.
Cell line: S49.1 / Production host: Escherichia coli (E. coli) / References: UniProt: P00860, ornithine decarboxylase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 421 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsSCHIFF-BASE LINK BETWEEN LYS_69_NZ AND PLP_69_C4A
Sequence detailsTHE ENZYME WHOSE STRUCTURE WAS SOLVED IS A TRUNCATED ENZYME AND DOES NOT CONTAIN RESIDUES 425 ...THE ENZYME WHOSE STRUCTURE WAS SOLVED IS A TRUNCATED ENZYME AND DOES NOT CONTAIN RESIDUES 425 THROUGH 461. RESIDUES WHICH ARE PRESENT IN THIS ENZYME, BUT WHICH HAD NO CORRESPONDING ELECTRON DENSITY ARE: 1, 30-35, 158-166, 298-310, AND 419-424.

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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: 37 %
Description: DATA WERE COLLECTED USING THE OSCILLATION METHOD
Crystal growpH: 6.5 / Details: pH 6.5
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion / Details: combination of vapor diffusion and gel
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112 mg/mlprotein1drop
22.5 mMdithiothreitol1drop
31.0 mMEDTA1drop
426 %(w/v)PEG33501drop
510 %(w/v)PEG33501reservoir

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Data collection

DiffractionMean temperature: 98 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.908
DetectorDetector: CCD / Date: Sep 1, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.908 Å / Relative weight: 1
ReflectionResolution: 1.6→27.92 Å / Num. obs: 49125 / % possible obs: 91.3 % / Redundancy: 5 % / Rmerge(I) obs: 0.081
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.188 / Mean I/σ(I) obs: 3.5 / % possible all: 75.4
Reflection shell
*PLUS
% possible obs: 75.4 %

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Processing

Software
NameClassification
MLPHAREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 1.6→27.9 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE PROGRAM USED FOR REFINEMENT WAS CCP PROGRAM SUITE: REFMAC_3.3 VERSION 3.4
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1995 4 %RANDOMLY SELECTED USING CCP PROGRAM SUITE: FREERFLAG VERSION 3.2
Rwork0.199 ---
obs-49125 91.3 %-
Refinement stepCycle: LAST / Resolution: 1.6→27.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3030 0 15 421 3466
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 27.9 Å / σ(F): 0 / % reflection Rfree: 4 % / Rfactor obs: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.01
X-RAY DIFFRACTIONp_angle_deg2.188
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_deg25.478
X-RAY DIFFRACTIONp_improper_angle_d
X-RAY DIFFRACTIONp_improper_angle_deg1.949

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