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- PDB-1d7k: CRYSTAL STRUCTURE OF HUMAN ORNITHINE DECARBOXYLASE AT 2.1 ANGSTRO... -

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Basic information

Entry
Database: PDB / ID: 1d7k
TitleCRYSTAL STRUCTURE OF HUMAN ORNITHINE DECARBOXYLASE AT 2.1 ANGSTROMS RESOLUTION
ComponentsHUMAN ORNITHINE DECARBOXYLASE
KeywordsLYASE / ALPHA-BETA BARREL / PYRIDOXAL 5'-PHOSPHATE / SHEET-DOMAIN / DECARBOXYLATION / ORNITHINE
Function / homology
Function and homology information


ornithine decarboxylase / putrescine biosynthetic process from arginine, via ornithine / ornithine decarboxylase activity / Metabolism of polyamines / polyamine metabolic process / Regulation of ornithine decarboxylase (ODC) / regulation of protein catabolic process / kidney development / response to virus / cell population proliferation ...ornithine decarboxylase / putrescine biosynthetic process from arginine, via ornithine / ornithine decarboxylase activity / Metabolism of polyamines / polyamine metabolic process / Regulation of ornithine decarboxylase (ODC) / regulation of protein catabolic process / kidney development / response to virus / cell population proliferation / positive regulation of cell population proliferation / 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
Ornithine decarboxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsAlmrud, J.J. / Oliveira, M.A. / Kern, A.D. / Grishin, N.V. / Phillips, M.A. / Hackert, M.L.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Crystal structure of human ornithine decarboxylase at 2.1 A resolution: structural insights to antizyme binding.
Authors: Almrud, J.J. / Oliveira, M.A. / Kern, A.D. / Grishin, N.V. / Phillips, M.A. / Hackert, M.L.
History
DepositionOct 18, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
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_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HUMAN ORNITHINE DECARBOXYLASE
B: HUMAN ORNITHINE DECARBOXYLASE


Theoretical massNumber of molelcules
Total (without water)94,3232
Polymers94,3232
Non-polymers00
Water7,224401
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5430 Å2
ΔGint-33 kcal/mol
Surface area34710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.680, 107.450, 139.710
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 HUMAN ORNITHINE DECARBOXYLASE


Mass: 47161.422 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organ: LIVER / Production host: Escherichia coli (E. coli) / References: UniProt: P11926, ornithine decarboxylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 401 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.86 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 7.5
Details: 20% PEG 3350, 0.2M NaCl, 5mM DTT, 0.1M Tris-HCl, pH 7.5, VAPOR DIFFUSION, temperature 16K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein11
220 %(w/v)PEG335012
30.1 MTris-HCl12
40.2 M12NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.908
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Jan 15, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.908 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 55799 / Num. obs: 53656 / % possible obs: 96.4 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 29 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 10.1
Reflection shellResolution: 2.09→2.16 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.363 / Num. unique all: 4929 / % possible all: 97.5
Reflection
*PLUS
Num. measured all: 223151
Reflection shell
*PLUS
% possible obs: 97.5 %

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Processing

Software
NameVersionClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
CCP4(SCALA)data scaling
RefinementResolution: 2.1→30.5 Å / Cross valid method: throyghout / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: This structure was refined using data from 30-2.1 angstrom resolution using the CCP4 suite program REFMAC. The REFMAC refinement was carried out using the maximum likelihood function and ...Details: This structure was refined using data from 30-2.1 angstrom resolution using the CCP4 suite program REFMAC. The REFMAC refinement was carried out using the maximum likelihood function and minimization by the conjugate direction method.
RfactorNum. reflection% reflectionSelection details
Rfree0.288 2789 5 %random
Rwork0.212 ---
all0.212 55799 --
obs-55799 --
Refinement stepCycle: LAST / Resolution: 2.1→30.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6423 0 0 401 6824
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.016
X-RAY DIFFRACTIONo_angle_deg2.5
Software
*PLUS
Name: REFMAC / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONp_bond_d
X-RAY DIFFRACTIONp_angle_deg
LS refinement shell
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 2.2 Å / Rfactor Rfree: 0.306 / Rfactor Rwork: 0.235 / Num. reflection obs: 6009

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