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- PDB-1szr: A Dimer interface mutant of ornithine decarboxylase reveals struc... -

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Basic information

Entry
Database: PDB / ID: 1szr
TitleA Dimer interface mutant of ornithine decarboxylase reveals structure of gem diamine intermediate
ComponentsOrnithine decarboxylase
KeywordsLYASE / pyridoxal phosphate / PXP / ODC / ornithine decarboxylase / gem-diamine / carbinolamine / dimer interface / beta-alpha-barrels / greek key
Function / homology
Function and homology information


ornithine decarboxylase / putrescine biosynthetic process from 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. / 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 ...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. / 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
Chem-ORX / Chem-PLG / PYRIDOXINE-5'-PHOSPHATE / Ornithine decarboxylase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsJackson, L.K. / Baldwin, J. / Goldsmith, E.J. / Phillips, M.A.
CitationJournal: Biochemistry / Year: 2004
Title: Multiple active site conformations revealed by distant site mutation in ornithine decarboxylase
Authors: Jackson, L.K. / Baldwin, J. / Akella, R. / Goldsmith, E.J. / Phillips, M.A.
History
DepositionApr 6, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 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_label_asym_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 23, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)189,1858
Polymers188,0174
Non-polymers1,1684
Water4,684260
1
C: Ornithine decarboxylase
D: Ornithine decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,5074
Polymers94,0092
Non-polymers4982
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5430 Å2
ΔGint-26 kcal/mol
Surface area29600 Å2
MethodPISA
2
A: Ornithine decarboxylase
B: Ornithine decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,6784
Polymers94,0092
Non-polymers6702
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-26 kcal/mol
Surface area28690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.468, 152.444, 155.007
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Ornithine decarboxylase / ODC


Mass: 47004.359 Da / Num. of mol.: 4 / Mutation: K294A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Species: Trypanosoma brucei / Strain: brucei / Plasmid: pODC29 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P07805, ornithine decarboxylase
#2: Chemical ChemComp-PXP / PYRIDOXINE-5'-PHOSPHATE


Mass: 249.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H12NO6P
#3: Chemical ChemComp-PLG / N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE] / N-PYRIDOXYL-GLYCINE-5-MONOPHOSPHATE


Mass: 306.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N2O7P
#4: 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.: 1 / Source method: obtained synthetically / Formula: C13H22N3O7P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.12 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Hepes, NaCl, NH4OAc, DTT, glycine, PEG 3350, D-ornithine, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 289.0K

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Data collection

DiffractionMean temperature: 124 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0332 Å
DetectorType: SBC-2 / Detector: CCD / Date: Apr 1, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.15→35 Å / Num. all: 89699 / Num. obs: 84756 / % possible obs: 94.5 % / Observed criterion σ(I): 1 / Redundancy: 5.3 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 21.1
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 3 % / Rmerge(I) obs: 0.558 / Mean I/σ(I) obs: 2.4 / Num. unique all: 8494 / % possible all: 96.1

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2TOD with ligands and Lys-294 removed

2tod


Resolution: 2.15→35 Å / Isotropic thermal model: isotropic / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.279 3484 -RANDOM
Rwork0.244 ---
all-87695 --
obs-68038 77.6 %-
Refinement stepCycle: LAST / Resolution: 2.15→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11057 0 76 260 11393
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0078
X-RAY DIFFRACTIONc_angle_deg1.238

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