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- PDB-5bwa: Crystal structure of ODC-PLP-AZ1 ternary complex -

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Basic information

Entry
Database: PDB / ID: 5bwa
TitleCrystal structure of ODC-PLP-AZ1 ternary complex
Components
  • Ornithine decarboxylase
  • Ornithine decarboxylase antizyme 1
KeywordsLyase/Lyase Inhibitor / Ornithine decarboxylase / Antizyme1 / Ornithine decarboxylase-Antizyme1 complex / polyamine biosynthesis / polyamine homeostasis / Lyase-Lyase Inhibitor complex
Function / homology
Function and homology information


negative regulation of polyamine transmembrane transport / ornithine decarboxylase / putrescine biosynthetic process from ornithine / ornithine decarboxylase activity / Metabolism of polyamines / polyamine metabolic process / polyamine biosynthetic process / positive regulation of intracellular protein transport / Regulation of ornithine decarboxylase (ODC) / regulation of protein catabolic process ...negative regulation of polyamine transmembrane transport / ornithine decarboxylase / putrescine biosynthetic process from ornithine / ornithine decarboxylase activity / Metabolism of polyamines / polyamine metabolic process / polyamine biosynthetic process / positive regulation of intracellular protein transport / Regulation of ornithine decarboxylase (ODC) / regulation of protein catabolic process / ornithine decarboxylase inhibitor activity / kidney development / response to virus / positive regulation of protein catabolic process / cell population proliferation / positive regulation of cell population proliferation / protein homodimerization activity / nucleus / cytoplasm / cytosol
Similarity search - Function
Aminopeptidase - #60 / Ornithine decarboxylase antizyme / Ornithine decarboxylase antizyme superfamily / Ornithine decarboxylase antizyme / Ornithine decarboxylase antizyme signature. / 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. ...Aminopeptidase - #60 / Ornithine decarboxylase antizyme / Ornithine decarboxylase antizyme superfamily / Ornithine decarboxylase antizyme / Ornithine decarboxylase antizyme signature. / 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. / 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 / Acyl-CoA N-acyltransferase / Aminopeptidase / TIM Barrel / Alpha-Beta Barrel / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Ornithine decarboxylase / Ornithine decarboxylase antizyme 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsWu, D.H.
CitationJournal: Sci Rep / Year: 2015
Title: Structural basis of Ornithine Decarboxylase inactivation and accelerated degradation by polyamine sensor Antizyme1
Authors: Wu, D.H. / Kaan, H.Y. / Zheng, X. / Tang, X. / He, Y. / Vanessa Tan, Q. / Zhang, N. / Song, H.
History
DepositionJun 7, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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 antizyme 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5473
Polymers69,3002
Non-polymers2471
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-12 kcal/mol
Surface area21580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.154, 74.084, 157.083
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ornithine decarboxylase / ODC


Mass: 51203.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ODC1 / Plasmid: pGEX-6p-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P11926, ornithine decarboxylase
#2: Protein Ornithine decarboxylase antizyme 1 / ODC-Az


Mass: 18097.234 Da / Num. of mol.: 1 / Fragment: UNP residues 69-228
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OAZ1, OAZ / Plasmid: pGEX-6p-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P54368
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P

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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: 2.23 Å3/Da / Density % sol: 44.88 %
Crystal growTemperature: 288 K / Method: evaporation / pH: 8.5 / Details: 0.2 M di-Ammonium tartrate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 13, 2014
RadiationMonochromator: X06SA / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→78.54 Å / Num. obs: 10195 / % possible obs: 94.7 % / Redundancy: 10 % / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 15.7
Reflection shellResolution: 3.2→3.27 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.667 / Mean I/σ(I) obs: 3.4 / % possible all: 94.4

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Processing

Software
NameVersionClassification
SCALAdata scaling
PHENIX(phenix.refine: 1.8.2_1309)refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1D7K, 1ZO0

1d7k

1zo0


Resolution: 3.2→42.759 Å / FOM work R set: 0.7417 / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2895 470 5.03 %
Rwork0.2288 17713 -
obs0.232 9326 94.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 184.48 Å2 / Biso mean: 65.32 Å2 / Biso min: 20 Å2
Refinement stepCycle: 1 / Resolution: 3.2→42.759 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3710 0 16 0 3726
Biso mean--48.6 --
Num. residues----471
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063817
X-RAY DIFFRACTIONf_angle_d1.2545167
X-RAY DIFFRACTIONf_chiral_restr0.088580
X-RAY DIFFRACTIONf_plane_restr0.006660
X-RAY DIFFRACTIONf_dihedral_angle_d18.8531388
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2001-3.36870.36431380.28852533267194
3.3687-3.57970.34971270.26372508263594
3.5797-3.85590.2611420.22622514265694
3.8559-4.24360.28871360.23112488262493
4.2436-4.85690.22651270.18862486261393
4.8569-6.11640.29991360.23982526266294
6.1164-42.76290.30361330.22592658279199
Refinement TLS params.Method: refined / Origin x: -13.6436 Å / Origin y: 3.7551 Å / Origin z: -17.5205 Å
111213212223313233
T0.348 Å2-0.037 Å20.083 Å2-0.2942 Å2-0.0654 Å2--0.2168 Å2
L1.4347 °2-0.4113 °2-0.8886 °2-1.56 °20.4924 °2--2.2173 °2
S0.0089 Å °-0.1634 Å °-0.0581 Å °0.1414 Å °-0.1145 Å °-0.0855 Å °0.1383 Å °-0.2437 Å °0.1448 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA19 - 600
2X-RAY DIFFRACTION1allB93 - 219

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