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2o4e

The solution structure of a protein-protein interaction module from a family 84 glycoside hydrolase of Clostridium perfringens

Method: SOLUTION NMR Dmax: 59.8 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

O-GlcNAcase nagJ

Clostridium perfringens

UniProt Q0TR53

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 768–909 Fragment：Putative protein-protein interaction module No other associated polymer SOLUTION NMR NMR measurement conditions：pH 7；298 K；Pressure 1 NMR sample composition：1mM U-15N,13C x82, 25mM hepes, 50mM nacl, 5mM cacl2, pH 7.0 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 2O4E Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2J62 Structure of a bacterial O-glcnacase in complex with glcnacstatin Deposited 2006-09-22 Different construct Different mutation/modification 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 31–624（594 aa） Fragment：RESIDUES 31-624
Chain B 31–624（594 aa） Fragment：RESIDUES 31-624
Not recorded CL CHLORIDE ION × 4 GSZ N-[(5R,6R,7R,8S)-6,7-DIHYDROXY-5-(HYDROXYMETHYL)-2-(2-PHENYLETHYL)-1,5,6,7,8,8A-HEXAHYDROIMIDAZO[1,2-A]PYRIDIN-8-YL]-2-METHYLPROPANAMIDE × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.26 Å R-free 0.219
2JH2 X-ray crystal structure of a cohesin-like module from Clostridium perfringens Deposited 2007-02-19 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 768–909（142 aa） Fragment：RESIDUES 768-909
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å R-free 0.295
2JH2 X-ray crystal structure of a cohesin-like module from Clostridium perfringens Deposited 2007-02-19 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 768–909（142 aa） Fragment：RESIDUES 768-909
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å R-free 0.295
2JH2 X-ray crystal structure of a cohesin-like module from Clostridium perfringens Deposited 2007-02-19 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 768–909（142 aa） Fragment：RESIDUES 768-909
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å R-free 0.295
2OZN The Cohesin-Dockerin Complex of NagJ and NagH from Clostridium perfringens Deposited 2007-02-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 768–909（142 aa） Fragment：Cohesin module (residues 768-909)
Not recorded CL CHLORIDE ION × 1 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.5；21% (w/v) polyethylene glycol 2000, 0.2M ammonium sulfate, 100mM sodium acetate, pH 4.5
Resolution 1.60 Å R-free 0.246
2V5C Family 84 glycoside hydrolase from Clostridium perfringens, 2.1 Angstrom structure Deposited 2008-10-02 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 31–624（594 aa） Fragment：CATALYTIC MODULE, RESIDUES 31-624
Not recorded CA CALCIUM ION × 2 CAC CACODYLATE ION × 3 NA SODIUM ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.10 Å R-free 0.255
2V5C Family 84 glycoside hydrolase from Clostridium perfringens, 2.1 Angstrom structure Deposited 2008-10-02 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 B 31–624（594 aa） Fragment：CATALYTIC MODULE, RESIDUES 31-624
Not recorded CA CALCIUM ION × 2 CAC CACODYLATE ION × 2 NA SODIUM ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.10 Å R-free 0.255
2V5D Structure of a Family 84 Glycoside Hydrolase and a Family 32 Carbohydrate-Binding Module in Tandem from Clostridium perfringens. Deposited 2008-10-02 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 31–767（737 aa） Fragment：RESIDUES 31-767
Not recorded CA CALCIUM ION × 3 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.30 Å R-free 0.370
2VUR Chemical dissection of the link between Streptozotocin, O-GlcNAc and pancreatic cell death Deposited 2008-05-29 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 31–624（594 aa） Fragment：O-GLCNACASE DOMAIN, RESIDUES 31-624
Not recorded YX1 2-deoxy-2-{[(2-hydroxy-1-methylhydrazino)carbonyl]amino}-beta-D-glucopyranose × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.20 Å R-free 0.241
2VUR Chemical dissection of the link between Streptozotocin, O-GlcNAc and pancreatic cell death Deposited 2008-05-29 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 B 31–624（594 aa） Fragment：O-GLCNACASE DOMAIN, RESIDUES 31-624
Not recorded YX1 2-deoxy-2-{[(2-hydroxy-1-methylhydrazino)carbonyl]amino}-beta-D-glucopyranose × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.20 Å R-free 0.241
2WB5 GlcNAcstatins are nanomolar inhibitors of human O-GlcNAcase inducing cellular hyper-O-GlcNAcylation Deposited 2009-02-20 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 31–624（594 aa） Fragment：O-GLCNACASE DOMAIN, RESIDUES 31-624
Not recorded CL CHLORIDE ION × 2 NA SODIUM ION × 1 VGB (5R,6R,7R,8S)-6,7-dihydroxy-5-(hydroxymethyl)-2-(2-phenylethyl)-8-(propanoylamino)-5,6,7,8-tetrahydro-1H-imidazo[1,2-a]pyridin-4-ium × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；30% PEG 8000, 0.2 M AMMONIUM SULFATE, 0.1 M SODIUM COCADYLATE, pH 6.5
Resolution 2.31 Å R-free 0.237
2WB5 GlcNAcstatins are nanomolar inhibitors of human O-GlcNAcase inducing cellular hyper-O-GlcNAcylation Deposited 2009-02-20 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 B 31–624（594 aa） Fragment：O-GLCNACASE DOMAIN, RESIDUES 31-624
Not recorded CL CHLORIDE ION × 3 VGB (5R,6R,7R,8S)-6,7-dihydroxy-5-(hydroxymethyl)-2-(2-phenylethyl)-8-(propanoylamino)-5,6,7,8-tetrahydro-1H-imidazo[1,2-a]pyridin-4-ium × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；30% PEG 8000, 0.2 M AMMONIUM SULFATE, 0.1 M SODIUM COCADYLATE, pH 6.5
Resolution 2.31 Å R-free 0.237
2X0Y Screening-based discovery of drug-like O-GlcNAcase inhibitor scaffolds Deposited 2009-12-18 Different construct Different mutation/modification 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 31–624（594 aa） Fragment：RESIDUES 31-624
Chain B 31–624（594 aa） Fragment：RESIDUES 31-624
Not recorded X0T 7-[(2S)-2,3-DIHYDROXYPROPYL]-1,3-DIMETHYL-3,7-DIHYDRO-1H-PURINE-2,6-DIONE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions 0.2 M AMMONIUM SULFATE, 0.1 M SODIUM CACODYLATE PH 6.5 AND 30 % PEG 8000 AND GAMMA-BUTYROLACTONE
Resolution 2.25 Å R-free 0.246
2XPK Cell-penetrant, nanomolar O-GlcNAcase inhibitors selective against lysosomal hexosaminidases Deposited 2010-08-26 Different construct Different mutation/modification 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 31–624（594 aa） Fragment：RESIDUES 31-624
Chain B 31–624（594 aa） Fragment：RESIDUES 31-624
Mutation：YES Mutation：YES Z0M N-[(5R,6R,7R,8S)-6,7-DIHYDROXY-5-(HYDROXYMETHYL)-2-(2-PHENYLETHYL)-5,6,7,8-TETRAHYDROIMIDAZO[1,2-A]PYRIDIN-8-YL]-3-SULFANYLPROPANAMIDE × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.40 Å R-free 0.242
2YDQ CpOGA D298N in complex with hOGA-derived O-GlcNAc peptide Deposited 2011-03-24 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 × 2 PDB declaration: dimeric
Chain A 31–618（588 aa） Fragment：RESIDUES 31-618
Mutation：YES CD CADMIUM ION × 19 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；0.6M NAAC, 0.175M CDSO4, 0.1M HEPES PH 7.5
Resolution 2.60 Å R-free 0.231
2YDR CpOGA D298N in complex with p53-derived O-GlcNAc peptide Deposited 2011-03-24 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 × 2 PDB declaration: dimeric
Chain A 31–618（588 aa） Fragment：RESIDUES 31-618
Mutation：YES CD CADMIUM ION × 18 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；0.6 M NAAC, 0.175 M CDSO4, 0.1 M HEPES PH 7.5
Resolution 2.75 Å R-free 0.219
2YDS CpOGA D298N in complex with TAB1-derived O-GlcNAc peptide Deposited 2011-03-24 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 × 2 PDB declaration: dimeric
Chain A 31–618（588 aa） Fragment：RESIDUES 31-618
Mutation：YES NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CD CADMIUM ION × 19 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；pH 8.5
Resolution 2.55 Å R-free 0.238
4ZXL CpOGA D298N in complex with Drosophila HCF -derived Thr-O-GlcNAc peptide Deposited 2015-05-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 39–617（579 aa） Fragment：UNP residues 39-617
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CD CADMIUM ION × 15 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295.15 K；CpOGA D298N was concentrated to 35 mg/ml in 25 mM Tris/HCl (pH 8.0) and crystallized from 0.175 M CdSO4 and 0.6 M sodium acetate pH 7.5
Resolution 2.60 Å R-free 0.220
5OXD Complex of a C. perfringens O-GlcNAcase with a fragment hit Deposited 2017-09-06 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 31–618（588 aa）
Not recorded CD CADMIUM ION × 22 B2W 5-(trifluoromethyl)-2,3-dihydro-1~{H}-1,4-diazepine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；Apo crystals were grown in 0.6 M NaAcetate pH 7.5, 0.175 M cadmium sulphate (ML). Crystals were then transferred into a drop supplemented with 10 mM ligand and incubated for 4 h. Crystals were cryo-protected by short immersion in ML supplemented with 20% glycerol and saturated with ligand.
Resolution 2.60 Å R-free 0.221
6RHE CpOGA D298N in complex with hOGA-derived S-GlcNAc peptide Deposited 2019-04-19 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 × 2 PDB declaration: dimeric
Chain A 31–619（589 aa）
Mutation：D298N CD CADMIUM ION × 25 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1:1 drops of proytein mixed with crystallisation buffer: 0.175 M CdSO4 and 0.6 M NaAc
Resolution 3.10 Å R-free 0.233
7KHV CpOGA IN COMPLEX WITH LIGAND 54 Deposited 2020-10-22 Different construct Different mutation/modification 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 31–624（594 aa）
Chain B 31–624（594 aa）
Mutation：D298N, V331C, N388D Mutation：D298N, V331C, N388D X1A N-(5-{[6-(5-methyl[1,2,4]triazolo[1,5-a]pyrimidin-7-yl)-2,6-diazaspiro[3.4]octan-2-yl]methyl}-1,3-thiazol-2-yl)acetamide × 2 CA CALCIUM ION × 1 SO4 SULFATE ION × 11 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.6；293 K；2.4M Ammonium Sulfate, 0.1M Hepes
Resolution 2.30 Å R-free 0.247
7KHV CpOGA IN COMPLEX WITH LIGAND 54 Deposited 2020-10-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 31–624（594 aa）
Chain D 31–624（594 aa）
Mutation：D298N, V331C, N388D Mutation：D298N, V331C, N388D X1A N-(5-{[6-(5-methyl[1,2,4]triazolo[1,5-a]pyrimidin-7-yl)-2,6-diazaspiro[3.4]octan-2-yl]methyl}-1,3-thiazol-2-yl)acetamide × 2 CA CALCIUM ION × 1 SO4 SULFATE ION × 15 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.6；293 K；2.4M Ammonium Sulfate, 0.1M Hepes
Resolution 2.30 Å R-free 0.247
7KHV CpOGA IN COMPLEX WITH LIGAND 54 Deposited 2020-10-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain E 31–624（594 aa）
Chain F 31–624（594 aa）
Mutation：D298N, V331C, N388D Mutation：D298N, V331C, N388D X1A N-(5-{[6-(5-methyl[1,2,4]triazolo[1,5-a]pyrimidin-7-yl)-2,6-diazaspiro[3.4]octan-2-yl]methyl}-1,3-thiazol-2-yl)acetamide × 2 CA CALCIUM ION × 1 SO4 SULFATE ION × 9 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.6；293 K；2.4M Ammonium Sulfate, 0.1M Hepes
Resolution 2.30 Å R-free 0.247

16 other PDB entries and 23 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name OGA_CLOP1
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 24–165； UniProt 768–909

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 2o4e

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2o4e
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2o4e
Deposition date deposition_date2006-12-04
Structure title titleThe solution structure of a protein-protein interaction module from a family 84 glycoside hydrolase of Clostridium perfringens
Keywords keywordsbeta-barrel, PROTEIN BINDING; PROTEIN BINDING
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier21.92 Å
Radius of gyration Rg (electron density) rg_electron21.36 Å
Forward intensity I(0) i01812110000.00
Molecular weight molecular_weight348140.0 kDa
Excluded volume excluded_volume430860 ų
Envelope volume envelope_volume131280 ų
Hydration-shell volume shell_volume33608 ų
Envelope diameter envelope_diameter116.9 Å
Shell Rg shell_rg38.07 Å
Envelope Rg envelope_rg36.34 Å
Shape Rg shape_rg21.35 Å
Total Rg total_rg21.79 Å
Total atoms total_atoms48520
Residues n_residues3300
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 dmax59.8 Å
Rg (real space) rg_real20.06 Å
Rg uncertainty (real space) rg_real_error0.15 Å
I(0) (real space) i0_real1.7210e+09
I(0) uncertainty (real space) i0_real_error1.9540e+07
Rg (reciprocal space) rg_reciprocal22.49 Å
I(0) (reciprocal space) i0_reciprocal1812000000.0000
Solution quality estimate total_estimate0.6588
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary18.7 Å
Skewness Skewness skewness0.508
Kurtosis Kurtosis kurtosis-0.423
Angular range angular_range— – 0.3600 Å−1
Current regularization parameter α current_alpha1.8770
Highest regularization parameter α highest_alpha1262000.0000
Real-space data points n_real_points68
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.003; Oscil: 0.909; Stabil: 0.992; Sysdev: 0.000; Positv: 1.000; Valcen: 0.870; Smooth: 0.000
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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) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd2o4ea1
Class classb — All beta proteins
Fold Fold foldb.2 — Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily Superfamily superfamilyb.2.2 — Carbohydrate-binding domain
Family Family familyb.2.2.2 — Cellulose-binding domain family III
Domain ID domain_idd2o4ea2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id2o4eA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily680 —
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8. Citations (1)

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9. Files and Curves (10)