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- PDB-1ord: CRYSTALLOGRAPHIC STRUCTURE OF A PLP-DEPENDENT ORNITHINE DECARBOXY... -

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Basic information

Entry
Database: PDB / ID: 1ord
TitleCRYSTALLOGRAPHIC STRUCTURE OF A PLP-DEPENDENT ORNITHINE DECARBOXYLASE FROM LACTOBACILLUS 30A TO 3.1 ANGSTROMS RESOLUTION
ComponentsORNITHINE DECARBOXYLASE
KeywordsCARBOXY-LYASE
Function / homology
Function and homology information


ornithine decarboxylase / ornithine decarboxylase activity / amino acid metabolic process / pyridoxal phosphate binding / cytosol
Similarity search - Function
Rossmann fold - #220 / Ornithine decarboxylase, N-terminal / Ornithine Decarboxylase; Chain A, domain 4 / Orn/Lys/Arg decarboxylase, C-terminal domain / Orn/Lys/Arg decarboxylase, N-terminal / Ornithine/lysine/arginine decarboxylase / Orn/Lys/Arg decarboxylase, N-terminal domain / Orn/Lys/Arg decarboxylases family 1 pyridoxal-P attachment site. / Orn/Lys/Arg decarboxylase, major domain / Orn/Lys/Arg decarboxylase, C-terminal ...Rossmann fold - #220 / Ornithine decarboxylase, N-terminal / Ornithine Decarboxylase; Chain A, domain 4 / Orn/Lys/Arg decarboxylase, C-terminal domain / Orn/Lys/Arg decarboxylase, N-terminal / Ornithine/lysine/arginine decarboxylase / Orn/Lys/Arg decarboxylase, N-terminal domain / Orn/Lys/Arg decarboxylases family 1 pyridoxal-P attachment site. / Orn/Lys/Arg decarboxylase, major domain / Orn/Lys/Arg decarboxylase, C-terminal / Orn/Lys/Arg decarboxylase, C-terminal domain superfamily / Orn/Lys/Arg decarboxylase, major domain / Orn/Lys/Arg decarboxylase, C-terminal domain / CheY-like superfamily / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Inducible ornithine decarboxylase
Similarity search - Component
Biological speciesLactobacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsHackert, M.L. / Momany, C. / Ernst, S. / Ghosh, R.
Citation
Journal: J.Mol.Biol. / Year: 1995
Title: Crystallographic structure of a PLP-dependent ornithine decarboxylase from Lactobacillus 30a to 3.0 A resolution.
Authors: Momany, C. / Ernst, S. / Ghosh, R. / Chang, N.L. / Hackert, M.L.
#1: Journal: J.Bacteriol. / Year: 1994
Title: Sequence of Ornithine Decarboxylase from Lactobacillus Sp. Strain 30A
Authors: Hackert, M.L. / Carroll, D.W. / Davidson, L. / Kim, S.-O. / Momany, C. / Vaaler, G.L. / Zhang, L.
History
DepositionFeb 8, 1995Processing site: BNL
Revision 1.0Sep 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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

Downloads & links

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Assembly

Deposited unit
A: ORNITHINE DECARBOXYLASE
B: ORNITHINE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,7944
Polymers165,2992
Non-polymers4942
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13280 Å2
ΔGint-59 kcal/mol
Surface area49210 Å2
MethodPISA
2
A: ORNITHINE DECARBOXYLASE
B: ORNITHINE DECARBOXYLASE
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)994,76124
Polymers991,79612
Non-polymers2,96612
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation5_555y,-x+y,z1
crystal symmetry operation6_555x-y,x,z1
Buried area107860 Å2
ΔGint-388 kcal/mol
Surface area267110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)195.600, 195.600, 97.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6
Atom site foot note1: CIS PROLINE - PRO A 128 / 2: CIS PROLINE - PRO A 661 / 3: CIS PROLINE - PRO A 662 / 4: CIS PROLINE - PRO B 128 / 5: CIS PROLINE - PRO B 661 / 6: CIS PROLINE - PRO B 662
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.797848, 0.602859, 0.000333), (0.602859, -0.797848, 0.000503), (0.000569, -0.000201, -1)
Vector: -0.025, 0.0521, 97.5712)

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Components

#1: Protein ORNITHINE DECARBOXYLASE


Mass: 82649.648 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Lactobacillus sp. (bacteria) / Strain: 30A / References: UniProt: P43099, ornithine decarboxylase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.26 Å3/Da / Density % sol: 62.26 %
Crystal grow
*PLUS
pH: 5.8 / Method: dialyzing
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17 %(w/v)PEG80001reservoir
250 mMpotassium phosphate1reservoir
3100 mM1reservoirKCl
40.5 mMEDTA1reservoir
50.05 %beta-octylglucoside1reservoir
60.02 %(w/v)1reservoirNaN3
70.2 mMpyridoxal-5'-phosphate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3→8 Å / Observed criterion σ(I): 4

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rfree: 0.268 / Rfactor Rwork: 0.219 / Rfactor obs: 0.219 / Highest resolution: 3 Å
Refinement stepCycle: LAST / Highest resolution: 3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11672 0 30 107 11809
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.898
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.76
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.72
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints
*PLUS
Type: x_dihedral_angle_d / Dev ideal: 24.767

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