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1oqy

Structure of the DNA repair protein hHR23a

Method: SOLUTION NMR Dmax: 245.9 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

UV excision repair protein RAD23 homolog A

Homo sapiens

UniProt P54725

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–363 Not recorded No other associated polymer SOLUTION NMR NMR measurement conditions：pH 6.5；298 K；Ionic strength (raw mmCIF value) 100 mM NaCl；Pressure 1 NMR sample composition：0.5 mM 13C,15N,2H hHR23a; 20 mM NaPO4 pH 6.5; 100 mM NaCl; 90% H2O, 10% D2O | 90% H2O/10% D2O Resolution not provided

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 1OQY Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1DV0 Refined NMR solution structure of the C-terminal UBA domain of the human homologue of RAD23A (HHR23A) Deposited 2000-01-19 Different construct Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 319–363（45 aa） Fragment：UBA DOMAIN (C-TERMINAL DOMAIN)
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；300 K；Ionic strength (raw mmCIF value) 50mM sodium phosphate, 100mM sodium chloride；Pressure ambient
NMR sample composition 1mM Uba-domain, chemically synthesized; 50mM potassium phosphate pH 6.5; 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition 2mM Uba-domain, expressed in E.coli, 50mM sodium phosphate, 100mM sodium chloride, 95% H2O, 5% D2O | 95% H2O/5% D2O
NMR sample composition 2mM Uba-domain, U-15N, 50mM sodium phosphate, 100mM sodium chloride, 95% H2O, 5% D2O | 95% H2O/5% D2O
NMR sample composition 2mM Uba-domain, U-15N,13C, 50mM sodium phosphate, 100mM sodium chloride, 95% H2O, 5% D2O | 95% H2O/5% D2O
Resolution not provided
1F4I SOLUTION STRUCTURE OF THE HHR23A UBA(2) MUTANT P333E, DEFICIENT IN BINDING THE HIV-1 ACCESSORY PROTEIN VPR Deposited 2000-06-07 Different construct Different mutation/modification Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 319–363（45 aa） Fragment：C-TERMINAL UBA DOMAIN
Mutation：P333E No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；300 K；Ionic strength (raw mmCIF value) 50mM sodium phosphate, 150mM sodium chloride；Pressure ambient
NMR sample composition 2mM UBA(2) domain mutant P333E; 50mM phosphate buffer, 150mM sodium chloride; 90% H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided
1IFY Solution Structure of the Internal UBA Domain of HHR23A Deposited 2001-04-13 Different construct Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 156–204（49 aa） Fragment：INTERNAL UBA DOMAIN
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；300 K；Ionic strength (raw mmCIF value) 50mM sodium phosphate, 100mM sodium chloride；Pressure ambient
NMR sample composition 2mM UBA1 U-15N,13C | 50mM phosphate buffer, 100mM sodium chloride 95% H2O, 5% D2O
NMR sample composition 2mM UBA1 U-15N | 50mM phosphate buffer, 100mM sodium chloride 95% H2O, 5% D2O
NMR sample composition 2mM UBA1 | 50mM phosphate buffer, 100mM sodium chloride 95% H2O, 5% D2O
Resolution not provided
1P98 High-resolution NMR structure of the Ubl-domain of HHR23A Deposited 2003-05-09 Different construct Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–78（78 aa） Fragment：Ubiquitin-like domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；300 K；Ionic strength (raw mmCIF value) 150mM；Pressure ambient
NMR sample composition 2mM ubiquitin-like domain of HHR23A U-15N,13C | 50mM sodium phosphate, 100mM sodium chloride, pH 6.5, 5% D2O
NMR sample composition 2mM ubiquitin-like domain of HHR23A, unlabeled | 50mM sodium phosphate, 100mM sodium chloride, pH 6.5, 5% D2O
Resolution not provided
1P9D High-resolution structure of the complex of HHR23A ubiquitin-like domain and the C-terminal ubiquitin-interacting motif of proteasome subunit S5a Deposited 2003-05-10 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain U 1–78（78 aa） Fragment：ubiquitin-like domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；300 K；Ionic strength (raw mmCIF value) 150mM；Pressure ambient
NMR sample composition 2mM S5a peptide unlabeled, 2mM ubiquitin-like domain of HHR23A U-15N,13C | 50mM sodium phosphate, 100mM sodium chloride, 5% D2O
NMR sample composition 2mM S5a peptide U-15N,13C, 2mM ubiquitin-like domain of HHR23A unlabeled | 50mM sodium phosphate, 100mM sodium chloride, 5% D2O
Resolution not provided
1QZE HHR23a protein structure based on residual dipolar coupling data Deposited 2003-09-16 Different construct Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–363（362 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 100 mM NaCl；Pressure 1
NMR sample composition 0.55 MM 15N, HHR23A; 20MM NAPO4 PH 6.5; 100 MM NACL;7.5 mg/ml Pf1 phage; 90% H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided
1TP4 Solution structure of the XPC binding domain of hHR23A protein Deposited 2004-06-15 Different construct Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 223–317（95 aa） Fragment：XPC binding domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.3；298 K；Ionic strength (raw mmCIF value) 20mM sodium phosphate, 122mM sodium chloride, 0.05% sodium azide；Pressure ambient
NMR sample composition 1mM XPCB U-15N,13C, 20mM sodium phosphate, 122mM sodium chloride, 0.05% sodium azide | 95% H2O/5% D2O
Resolution not provided
2WYQ THE CRYSTAL STRUCTURE OF THE UBIQUITIN-LIKE (UBL) DOMAIN OF HHR23A (HUMAN HOMOLOGUE A OF RAD23) Deposited 2009-11-19 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–82（82 aa） Fragment：UBIQUITIN-LIKE DOMAIN, RESIDUES 1-82
Not recorded SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；0.1 M HEPES PH 7.5, 2% PEG 400 AND 2.0 M AMMONIUM SULFATE, AT ROOM TEMPERATURE
Resolution 1.65 Å R-free 0.160
2WYQ THE CRYSTAL STRUCTURE OF THE UBIQUITIN-LIKE (UBL) DOMAIN OF HHR23A (HUMAN HOMOLOGUE A OF RAD23) Deposited 2009-11-19 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–82（82 aa） Fragment：UBIQUITIN-LIKE DOMAIN, RESIDUES 1-82
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；0.1 M HEPES PH 7.5, 2% PEG 400 AND 2.0 M AMMONIUM SULFATE, AT ROOM TEMPERATURE
Resolution 1.65 Å R-free 0.160
5XBO Lanthanoid tagging via an unnatural amino acid for protein structure characterization Deposited 2017-03-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 156–204（49 aa） Fragment：UNP residues 156-204
Not recorded TB TERBIUM(III) ION × 1 SOLUTION NMR
NMR measurement conditions pH 7.2；298 K；Ionic strength (raw mmCIF value) 100；Pressure 760
NMR sample composition 20mM HEPES, 100mM sodium chloride, 10% D2O, 0.2mM [U-99% 15N] ubiquitin, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 20mM HEPES, 100mM sodium chloride, 0.1mM [U-99% 15N] HHR23A UBA1 Domain, 0.1 mM ubiquitin, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
6W2G Crystal Structure of Y188G Variant of the Internal UBA Domain of HHR23A in Monoclinic Unit Cell Deposited 2020-03-05 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 155–204（50 aa）
Mutation：Y188G EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2M Ammonium sulfate, 0.1M Phosphate-citrate pH 4.2, 40%(v/v) Ethylene glycol
Resolution 1.10 Å R-free 0.153
6W2G Crystal Structure of Y188G Variant of the Internal UBA Domain of HHR23A in Monoclinic Unit Cell Deposited 2020-03-05 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 155–204（50 aa）
Mutation：Y188G EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2M Ammonium sulfate, 0.1M Phosphate-citrate pH 4.2, 40%(v/v) Ethylene glycol
Resolution 1.10 Å R-free 0.153
6W2H Crystal Structure of the Internal UBA Domain of HHR23A Deposited 2020-03-05 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 155–204（50 aa）
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1M Tris pH 8.5, 1.5 M Ammonium sulfate, 12%(v/v) Glycerol
Resolution 1.60 Å R-free 0.205
6W2I Crystal Structure of Y188G Variant of the Internal UBA Domain of HHR23A Deposited 2020-03-05 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 155–204（50 aa）
Mutation：Y188G GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2.0M Ammonium sulfate
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2.0M Ammonium sulfate
Resolution 1.45 Å R-free 0.183
6XQI Structure of HIV-1 Vpr in complex with the human nucleotide excision repair protein hHR23A Deposited 2020-07-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain F 319–358（40 aa）
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1M Tris, pH 7.5, 10% PEG 4000
Resolution 2.34 Å R-free 0.220
6XQI Structure of HIV-1 Vpr in complex with the human nucleotide excision repair protein hHR23A Deposited 2020-07-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain G 319–358（40 aa）
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1M Tris, pH 7.5, 10% PEG 4000
Resolution 2.34 Å R-free 0.220
6XQJ Structure of HIV-1 Vpr in complex with the human nucleotide excision repair protein hHR23A Deposited 2020-07-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 223–363（141 aa）
Not recorded ZN ZINC ION × 1 SOLUTION NMR
NMR measurement conditions pH 7.2；298 K；Ionic strength (raw mmCIF value) 100；Pressure 1
NMR measurement conditions pH 7.5；298 K；Ionic strength (raw mmCIF value) 100；Pressure 1
NMR sample composition 927 uM [U-100% 2H; U-100% 13C; U-100% 15N] Vpr-hHR23A complex, 25 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 1 mM TCEP, 0.1 mM ZnSO4, 0.1 mM EDTA, 0.02 % sodium azide, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition 1100 uM [U-100% 13C; U-100% 15N] Vpr-hHR23A complex, 25 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 1 mM TCEP, 0.1 mM ZnSO4, 0.1 mM EDTA, 0.02 % sodium azide, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition 1110 uM [U-100% 15N] Vpr-hHR23A complex, 25 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 1 mM TCEP, 0.1 mM ZnSO4, 0.1 mM EDTA, 0.02 % sodium azide, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition 1000 uM [U-100% 15N] Vpr-hHR23A complex, 25 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 1 mM TCEP, 0.1 mM ZnSO4, 0.1 mM EDTA, 0.02 % sodium azide, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition 745 uM [U-100% 13C; U-100% 15N] Vpr-hHR23A complex, 25 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 1 mM TCEP, 0.1 mM ZnSO4, 0.1 mM EDTA, 0.02 % sodium azide, 93% H2O/7% D2O | 93% H2O/7% D2O
Resolution not provided
7TGP E176T/Y188G variant of the internal UBA Domain of HHR23A Deposited 2022-01-08 Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 155–204（50 aa） Fragment：residues 154-204 of the Internal UBA domain
Mutation：E176T, Y188G No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；sodium formate
Resolution 1.40 Å R-free 0.175
8Q06 EF-hand of MINDY3 Deubiquitylase in Complex with UBL of RAD23A Deposited 2023-07-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–84（84 aa）
Chain D 1–84（84 aa）
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M potassium chloride, 2.2 M ammonium sulphate
Resolution 1.90 Å R-free 0.247

16 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RD23A_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 6–368； UniProt 1–363

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 1oqy

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1oqy
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1oqy
Deposition date deposition_date2003-03-11
Structure title titleStructure of the DNA repair protein hHR23a
Keywords keywordsDNA repair, proteasome-mediated degradation, protein-protein interaction, REPLICATION; REPLICATION
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier69.79 Å
Radius of gyration Rg (electron density) rg_electron69.83 Å
Forward intensity I(0) i03392020000.00
Molecular weight molecular_weight474260.0 kDa
Excluded volume excluded_volume587220 ų
Envelope volume envelope_volume1269700 ų
Hydration-shell volume shell_volume152530 ų
Envelope diameter envelope_diameter248.4 Å
Shell Rg shell_rg68.13 Å
Envelope Rg envelope_rg68.74 Å
Shape Rg shape_rg69.85 Å
Total Rg total_rg69.70 Å
Total atoms total_atoms65808
Residues n_residues4356
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax245.9 Å
Rg (real space) rg_real72.86 Å
Rg uncertainty (real space) rg_real_error1.26 Å
I(0) (real space) i0_real3.3970e+09
I(0) uncertainty (real space) i0_real_error6.6100e+07
Rg (reciprocal space) rg_reciprocal69.92 Å
I(0) (reciprocal space) i0_reciprocal3393000000.0000
Solution quality estimate total_estimate0.8981
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary78.2 Å
Skewness Skewness skewness0.524
Kurtosis Kurtosis kurtosis0.139
Angular range angular_range— – 0.1100 Å−1
Current regularization parameter α current_alpha1.0860
Highest regularization parameter α highest_alpha525300000.0000
Real-space data points n_real_points23
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.814; Stabil: 0.885; Sysdev: 1.000; Positv: 1.000; Valcen: 0.956; Smooth: 0.643
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd1oqya1
Class classa — All alpha proteins
Fold Fold folda.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamilya.5.2 — UBA-like
Family Family familya.5.2.1 — UBA domain
Domain ID domain_idd1oqya2
Class classa — All alpha proteins
Fold Fold folda.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamilya.5.2 — UBA-like
Family Family familya.5.2.1 — UBA domain
Domain ID domain_idd1oqya3
Class classa — All alpha proteins
Fold Fold folda.189 — XPC-binding domain-like
Superfamily Superfamily superfamilya.189.1 — XPC-binding domain
Family Family familya.189.1.1 — XPC-binding domain
Domain ID domain_idd1oqya4
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.1 — Ubiquitin-related

CATH v4.4 (4 domains)

Domain ID domain_id1oqyA01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id1oqyA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily10 — Ubiquitin-associated (UBA) domain
Domain ID domain_id1oqyA03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily540 — XPC-binding domain
Domain ID domain_id1oqyA04
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily10 — Ubiquitin-associated (UBA) domain
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8. Citations (1)

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9. Files and Curves (10)