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- PDB-7u6p: Structure of an intellectual disability-associated ornithine deca... -

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Basic information

Entry
Database: PDB / ID: 7u6p
TitleStructure of an intellectual disability-associated ornithine decarboxylase variant G84R
ComponentsOrnithine decarboxylase
KeywordsHYDROLASE / ornithine decarboxylase / intellectual disability-associated variant
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 / cytosol / cytoplasm
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 / Alanine racemase/group IV decarboxylase, C-terminal / PLP-binding barrel
Similarity search - Domain/homology
PHOSPHATE ION / Ornithine decarboxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsZhou, X.E. / Schultz, C.R. / Powell, K.S. / Henrickson, A. / Lamp, J. / Brunzelle, J.S. / Demeler, B. / Vega, I.E. / Bachmann, A.S. / Melcher, K.
Funding support United States, Canada, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM120600 United States
Canada Research ChairsC150-2017-00015 Canada
Canada Foundation for InnovationCFI-37589 Canada
CitationJournal: Acs Omega / Year: 2022
Title: Structure and Enzymatic Activity of an Intellectual Disability-Associated Ornithine Decarboxylase Variant, G84R.
Authors: Zhou, X.E. / Schultz, C.R. / Suino Powell, K. / Henrickson, A. / Lamp, J. / Brunzelle, J.S. / Demeler, B. / Vega, I.E. / Bachmann, A.S. / Melcher, K.
History
DepositionMar 4, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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
A: Ornithine decarboxylase
B: Ornithine decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,8734
Polymers94,6842
Non-polymers1902
Water5,441302
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5440 Å2
ΔGint-47 kcal/mol
Surface area33350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.806, 85.879, 154.738
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: 47341.754 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: G84R variant / Source: (gene. exp.) Homo sapiens (human) / Gene: ODC1 / Production host: Escherichia coli (E. coli) / References: UniProt: P11926, ornithine decarboxylase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.62 Å3/Da / Density % sol: 53.14 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium acetate trihydrate pH 7.0, 20% w/v polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→45.6 Å / Num. obs: 42293 / % possible obs: 99.9 % / Redundancy: 9.4 % / CC1/2: 0.993 / Net I/σ(I): 8.5
Reflection shellResolution: 2.35→2.43 Å / Rmerge(I) obs: 1.35 / Num. unique obs: 4104 / CC1/2: 0.87

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7S3F

7s3f


Resolution: 2.35→42.464 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2245 2991 7.08 %
Rwork0.1882 39231 -
obs0.1907 42222 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.87 Å2 / Biso mean: 37.6127 Å2 / Biso min: 10.64 Å2
Refinement stepCycle: final / Resolution: 2.35→42.464 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6367 0 10 302 6679
Biso mean--35.06 38.78 -
Num. residues----813
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036528
X-RAY DIFFRACTIONf_angle_d0.6538837
X-RAY DIFFRACTIONf_dihedral_angle_d15.9973910
X-RAY DIFFRACTIONf_chiral_restr0.045976
X-RAY DIFFRACTIONf_plane_restr0.0041138
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.35-2.38860.29461370.23581860100
2.3886-2.42970.30091400.22871849100
2.4297-2.47390.25941340.22661823100
2.4739-2.52150.27411230.22931860100
2.5215-2.5730.26931240.23611873100
2.573-2.62890.30571410.2237181099
2.6289-2.690.28221560.22331840100
2.69-2.75730.26071570.21911844100
2.7573-2.83180.26481320.22351844100
2.8318-2.91510.30281670.21671836100
2.9151-3.00920.24461600.20321842100
3.0092-3.11670.24171310.19921867100
3.1167-3.24150.20691530.19441849100
3.2415-3.38890.25211330.19251860100
3.3889-3.56750.22671280.19291904100
3.5675-3.79090.21841300.17681878100
3.7909-4.08340.21281370.16581894100
4.0834-4.49390.16041470.14971863100
4.4939-5.14320.18121390.1436189199
5.1432-6.47620.19391540.18821929100
6.4762-42.40.17971680.167201599

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