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- PDB-7u6u: Structure of an intellectual disability-associated ornithine deca... -

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Basic information

Entry
Database: PDB / ID: 7u6u
TitleStructure of an intellectual disability-associated ornithine decarboxylase variant G84R in complex with PLP
ComponentsOrnithine decarboxylase
KeywordsHYDROLASE / ornithine decarboxylase / intellectual disability-associated variant
Function / homology
Function and homology information


putrescine biosynthetic process from ornithine / ornithine decarboxylase / 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 ...putrescine biosynthetic process from ornithine / ornithine decarboxylase / 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. / 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 ...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 / Alanine racemase/group IV decarboxylase, C-terminal / PLP-binding barrel
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Ornithine decarboxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 6, 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)95,1784
Polymers94,6842
Non-polymers4942
Water9,962553
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6090 Å2
ΔGint-27 kcal/mol
Surface area32960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.147, 86.098, 153.277
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-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


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


Mass: 18.015 Da / Num. of mol.: 553 / 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: 2.72 Å3/Da / Density % sol: 54.79 %
Crystal growTemperature: 277 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 EIGER2 S 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: 1.85→50 Å / Num. obs: 84340 / % possible obs: 99.9 % / Redundancy: 6.9 % / CC1/2: 0.996 / Net I/σ(I): 11.4
Reflection shellResolution: 1.85→1.88 Å / Num. unique obs: 4377 / CC1/2: 0.62

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Processing

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

7s3f


Resolution: 1.85→43.049 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2036 5905 7.01 %
Rwork0.1806 78344 -
obs0.1822 84249 99.81 %
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.32 Å2 / Biso mean: 28.1147 Å2 / Biso min: 9.42 Å2
Refinement stepCycle: final / Resolution: 1.85→43.049 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6295 0 30 553 6878
Biso mean--22.31 37.33 -
Num. residues----802
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056485
X-RAY DIFFRACTIONf_angle_d0.8488782
X-RAY DIFFRACTIONf_dihedral_angle_d16.3543871
X-RAY DIFFRACTIONf_chiral_restr0.054965
X-RAY DIFFRACTIONf_plane_restr0.0061128
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.85-1.8710.28191860.25352567100
1.871-1.89310.26421960.23962595100
1.8931-1.91610.29142100.22512537100
1.9161-1.94040.23241980.21462559100
1.9404-1.96590.2392190.20472568100
1.9659-1.99290.2231880.19452600100
1.9929-2.02130.24881910.20292562100
2.0213-2.05150.22722030.20142607100
2.0515-2.08360.21791750.20262551100
2.0836-2.11770.2312100.20722601100
2.1177-2.15420.22372240.1932546100
2.1542-2.19340.24951930.19592617100
2.1934-2.23560.21561710.19252589100
2.2356-2.28120.23511860.18572603100
2.2812-2.33080.20182180.18732598100
2.3308-2.3850.20622080.18432586100
2.385-2.44470.21961840.1842614100
2.4447-2.51080.21271650.18782623100
2.5108-2.58460.21612210.18822592100
2.5846-2.6680.21641920.1842601100
2.668-2.76340.21051930.18882640100
2.7634-2.8740.20531740.17682629100
2.874-3.00480.19941970.17932614100
3.0048-3.16320.172000.172631100
3.1632-3.36130.17161960.1692643100
3.3613-3.62070.18452040.17262599
3.6207-3.98480.17812030.1598262099
3.9848-4.56090.18111900.14992698100
4.5609-5.7440.17162070.16612701100
5.744-430.20822030.17922827100

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