SAXSdb — 9y4u

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Glyceraldehyde-3-phosphate dehydrogenase

Neisseria gonorrhoeae NCCP11945

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 24–357 Chain B； UniProt 24–357	Fragment：residues 24-357	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 4.5；291 K；Berkeley D4: 25% (w/v) PEG 3350, 100 mM sodium acetate pH 4.5. 2mM NAD addied prior to crystallization, plate 20205 well D4 drop 3 , Puck: PSL2003, Cryo: 80% crystallant + 20% PEG 200	Resolution 1.90 Å R-free 0.214

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 9Y4U	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5VMT Crystal structure of a glyceraldehyde-3-phosphate dehydrogenase from Neisseria gonorrhoeae bound to NAD Deposited 2017-04-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 24–357（334 aa） Fragment：residues 24-357 Chain B 24–357（334 aa） Fragment：residues 24-357 Chain C 24–357（334 aa） Fragment：residues 24-357 Chain D 24–357（334 aa） Fragment：residues 24-357	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 CL CHLORIDE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；NegoA.00617.a.B1.PS38018 at 21.2 mg/mL with 3 mM NAD against JCSG+ screen condition A9 0.2 M ammonium chloride, 25% PEG 3350 supplemented with 20% ethylene glycol and 3 mM NAD as cryoprotectant, crystal tracking ID 284230a9, unique puck ID giy4-10	Resolution 2.50 Å R-free 0.219
5VMT Crystal structure of a glyceraldehyde-3-phosphate dehydrogenase from Neisseria gonorrhoeae bound to NAD Deposited 2017-04-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain E 24–357（334 aa） Fragment：residues 24-357 Chain F 24–357（334 aa） Fragment：residues 24-357 Chain G 24–357（334 aa） Fragment：residues 24-357 Chain H 24–357（334 aa） Fragment：residues 24-357	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；NegoA.00617.a.B1.PS38018 at 21.2 mg/mL with 3 mM NAD against JCSG+ screen condition A9 0.2 M ammonium chloride, 25% PEG 3350 supplemented with 20% ethylene glycol and 3 mM NAD as cryoprotectant, crystal tracking ID 284230a9, unique puck ID giy4-10	Resolution 2.50 Å R-free 0.219
9Z9C Crystal structure of a glyceraldehyde-3-phosphate dehydrogenase from Neisseria gonorrhoeae in complex with NAD (P1 form) Deposited 2025-11-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 24–357（334 aa） Fragment：residues 24-357 Chain B 24–357（334 aa） Fragment：residues 24-357 Chain C 24–357（334 aa） Fragment：residues 24-357 Chain D 24–357（334 aa） Fragment：residues 24-357	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；Berkeley D8 : 25% PEG 3350, 0.10M MES pH 5.5, 5% iso-Propanol, 0.10M ammonium citrate dibasic. NegoA.00617.a.B1.PS38018 at 8 mg/mL. plate 20061 D8 drop 1, Puck: PSL-2202, Cryo: 80% crystallant + 20% PEG 200	Resolution 2.30 Å R-free 0.232
9Z9C Crystal structure of a glyceraldehyde-3-phosphate dehydrogenase from Neisseria gonorrhoeae in complex with NAD (P1 form) Deposited 2025-11-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain E 24–357（334 aa） Fragment：residues 24-357 Chain F 24–357（334 aa） Fragment：residues 24-357 Chain G 24–357（334 aa） Fragment：residues 24-357 Chain H 24–357（334 aa） Fragment：residues 24-357	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 PGE TRIETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；Berkeley D8 : 25% PEG 3350, 0.10M MES pH 5.5, 5% iso-Propanol, 0.10M ammonium citrate dibasic. NegoA.00617.a.B1.PS38018 at 8 mg/mL. plate 20061 D8 drop 1, Puck: PSL-2202, Cryo: 80% crystallant + 20% PEG 200	Resolution 2.30 Å R-free 0.232
9Z9C Crystal structure of a glyceraldehyde-3-phosphate dehydrogenase from Neisseria gonorrhoeae in complex with NAD (P1 form) Deposited 2025-11-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain I 24–357（334 aa） Fragment：residues 24-357 Chain J 24–357（334 aa） Fragment：residues 24-357 Chain K 24–357（334 aa） Fragment：residues 24-357 Chain L 24–357（334 aa） Fragment：residues 24-357	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；Berkeley D8 : 25% PEG 3350, 0.10M MES pH 5.5, 5% iso-Propanol, 0.10M ammonium citrate dibasic. NegoA.00617.a.B1.PS38018 at 8 mg/mL. plate 20061 D8 drop 1, Puck: PSL-2202, Cryo: 80% crystallant + 20% PEG 200	Resolution 2.30 Å R-free 0.232
9Z9C Crystal structure of a glyceraldehyde-3-phosphate dehydrogenase from Neisseria gonorrhoeae in complex with NAD (P1 form) Deposited 2025-11-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain M 24–357（334 aa） Fragment：residues 24-357 Chain N 24–357（334 aa） Fragment：residues 24-357 Chain O 24–357（334 aa） Fragment：residues 24-357 Chain P 24–357（334 aa） Fragment：residues 24-357	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；Berkeley D8 : 25% PEG 3350, 0.10M MES pH 5.5, 5% iso-Propanol, 0.10M ammonium citrate dibasic. NegoA.00617.a.B1.PS38018 at 8 mg/mL. plate 20061 D8 drop 1, Puck: PSL-2202, Cryo: 80% crystallant + 20% PEG 200	Resolution 2.30 Å R-free 0.232
9Z9C Crystal structure of a glyceraldehyde-3-phosphate dehydrogenase from Neisseria gonorrhoeae in complex with NAD (P1 form) Deposited 2025-11-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain Q 24–357（334 aa） Fragment：residues 24-357 Chain R 24–357（334 aa） Fragment：residues 24-357 Chain S 24–357（334 aa） Fragment：residues 24-357 Chain T 24–357（334 aa） Fragment：residues 24-357	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；Berkeley D8 : 25% PEG 3350, 0.10M MES pH 5.5, 5% iso-Propanol, 0.10M ammonium citrate dibasic. NegoA.00617.a.B1.PS38018 at 8 mg/mL. plate 20061 D8 drop 1, Puck: PSL-2202, Cryo: 80% crystallant + 20% PEG 200	Resolution 2.30 Å R-free 0.232
9Z9C Crystal structure of a glyceraldehyde-3-phosphate dehydrogenase from Neisseria gonorrhoeae in complex with NAD (P1 form) Deposited 2025-11-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain U 24–357（334 aa） Fragment：residues 24-357 Chain V 24–357（334 aa） Fragment：residues 24-357 Chain W 24–357（334 aa） Fragment：residues 24-357 Chain X 24–357（334 aa） Fragment：residues 24-357	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；Berkeley D8 : 25% PEG 3350, 0.10M MES pH 5.5, 5% iso-Propanol, 0.10M ammonium citrate dibasic. NegoA.00617.a.B1.PS38018 at 8 mg/mL. plate 20061 D8 drop 1, Puck: PSL-2202, Cryo: 80% crystallant + 20% PEG 200	Resolution 2.30 Å R-free 0.232
9ZAG Crystal structure of a glyceraldehyde-3-phosphate dehydrogenase from Neisseria gonorrhoeae in complex with NAD and GLYCERALDEHYDE-3-PHOSPHATE Deposited 2025-11-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 24–357（334 aa） Chain B 24–357（334 aa） Chain C 24–357（334 aa） Chain D 24–357（334 aa）	Not recorded	G3H GLYCERALDEHYDE-3-PHOSPHATE × 4 PEG DI(HYDROXYETHYL)ETHER × 5 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 NA SODIUM ION × 4 PGE TRIETHYLENE GLYCOL × 1 CL CHLORIDE ION × 1 GOL GLYCEROL × 2 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；Berkeley H9: 25% PEG 4000, 0.10M HEPES pH 7.5, 10% iso-Propanol. NegoA.00617.a.B1.PS38018 at 8 mg/mL. cocrystallization with NAD and G3H, plate 20061 H9 drop 1, Puck: PSL-2203, Cryo: 80% crystallant + 20% PEG 200	Resolution 1.91 Å R-free 0.187
9ZAG Crystal structure of a glyceraldehyde-3-phosphate dehydrogenase from Neisseria gonorrhoeae in complex with NAD and GLYCERALDEHYDE-3-PHOSPHATE Deposited 2025-11-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain E 24–357（334 aa） Chain F 24–357（334 aa） Chain G 24–357（334 aa） Chain H 24–357（334 aa）	Not recorded	G3H GLYCERALDEHYDE-3-PHOSPHATE × 4 PEG DI(HYDROXYETHYL)ETHER × 3 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 NA SODIUM ION × 4 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；Berkeley H9: 25% PEG 4000, 0.10M HEPES pH 7.5, 10% iso-Propanol. NegoA.00617.a.B1.PS38018 at 8 mg/mL. cocrystallization with NAD and G3H, plate 20061 H9 drop 1, Puck: PSL-2203, Cryo: 80% crystallant + 20% PEG 200	Resolution 1.91 Å R-free 0.187
9ZAO Crystal structure of a glyceraldehyde-3-phosphate dehydrogenase from Neisseria gonorrhoeae in complex with NAD (P1 form2) Deposited 2025-11-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 24–357（334 aa） Chain B 24–357（334 aa） Chain C 24–357（334 aa） Chain D 24–357（334 aa）	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 3 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；Morpheus Fusion, B4 : 20 mM Sodium formate, 20 mM Ammonium acetate, 20 mM Sodium citrate tribasic dihydrate, 20 mM Potassium sodium tartrate tetrahydrate, 20 mM Sodium oxamate, 0.12 M Ethyleneglycol 40 mM Imidazole, 60 mM MES monohydrate (acid), pH 6.5, 20% v/v PEG 500 MME, 10 % w/v PEG 20000, 10% iso-Propanol. NegoA.00617.a.B1.PS38018 at 8 mg/mL. cocrystallization with NAD, plate 20064 B4 drop 1, Puck: PSL-2206, Cryo: direct	Resolution 3.09 Å R-free 0.234
9ZAO Crystal structure of a glyceraldehyde-3-phosphate dehydrogenase from Neisseria gonorrhoeae in complex with NAD (P1 form2) Deposited 2025-11-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain E 24–357（334 aa） Chain F 24–357（334 aa） Chain G 24–357（334 aa） Chain H 24–357（334 aa）	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 3 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；Morpheus Fusion, B4 : 20 mM Sodium formate, 20 mM Ammonium acetate, 20 mM Sodium citrate tribasic dihydrate, 20 mM Potassium sodium tartrate tetrahydrate, 20 mM Sodium oxamate, 0.12 M Ethyleneglycol 40 mM Imidazole, 60 mM MES monohydrate (acid), pH 6.5, 20% v/v PEG 500 MME, 10 % w/v PEG 20000, 10% iso-Propanol. NegoA.00617.a.B1.PS38018 at 8 mg/mL. cocrystallization with NAD, plate 20064 B4 drop 1, Puck: PSL-2206, Cryo: direct	Resolution 3.09 Å R-free 0.234
9ZAO Crystal structure of a glyceraldehyde-3-phosphate dehydrogenase from Neisseria gonorrhoeae in complex with NAD (P1 form2) Deposited 2025-11-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain I 24–357（334 aa） Chain J 24–357（334 aa） Chain K 24–357（334 aa） Chain L 24–357（334 aa）	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；Morpheus Fusion, B4 : 20 mM Sodium formate, 20 mM Ammonium acetate, 20 mM Sodium citrate tribasic dihydrate, 20 mM Potassium sodium tartrate tetrahydrate, 20 mM Sodium oxamate, 0.12 M Ethyleneglycol 40 mM Imidazole, 60 mM MES monohydrate (acid), pH 6.5, 20% v/v PEG 500 MME, 10 % w/v PEG 20000, 10% iso-Propanol. NegoA.00617.a.B1.PS38018 at 8 mg/mL. cocrystallization with NAD, plate 20064 B4 drop 1, Puck: PSL-2206, Cryo: direct	Resolution 3.09 Å R-free 0.234
9ZAO Crystal structure of a glyceraldehyde-3-phosphate dehydrogenase from Neisseria gonorrhoeae in complex with NAD (P1 form2) Deposited 2025-11-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain M 24–357（334 aa） Chain N 24–357（334 aa） Chain O 24–357（334 aa） Chain P 24–357（334 aa）	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；Morpheus Fusion, B4 : 20 mM Sodium formate, 20 mM Ammonium acetate, 20 mM Sodium citrate tribasic dihydrate, 20 mM Potassium sodium tartrate tetrahydrate, 20 mM Sodium oxamate, 0.12 M Ethyleneglycol 40 mM Imidazole, 60 mM MES monohydrate (acid), pH 6.5, 20% v/v PEG 500 MME, 10 % w/v PEG 20000, 10% iso-Propanol. NegoA.00617.a.B1.PS38018 at 8 mg/mL. cocrystallization with NAD, plate 20064 B4 drop 1, Puck: PSL-2206, Cryo: direct	Resolution 3.09 Å R-free 0.234
9ZAO Crystal structure of a glyceraldehyde-3-phosphate dehydrogenase from Neisseria gonorrhoeae in complex with NAD (P1 form2) Deposited 2025-11-19	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain Q 24–357（334 aa） Chain R 24–357（334 aa） Chain S 24–357（334 aa） Chain T 24–357（334 aa）	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；Morpheus Fusion, B4 : 20 mM Sodium formate, 20 mM Ammonium acetate, 20 mM Sodium citrate tribasic dihydrate, 20 mM Potassium sodium tartrate tetrahydrate, 20 mM Sodium oxamate, 0.12 M Ethyleneglycol 40 mM Imidazole, 60 mM MES monohydrate (acid), pH 6.5, 20% v/v PEG 500 MME, 10 % w/v PEG 20000, 10% iso-Propanol. NegoA.00617.a.B1.PS38018 at 8 mg/mL. cocrystallization with NAD, plate 20064 B4 drop 1, Puck: PSL-2206, Cryo: direct	Resolution 3.09 Å R-free 0.234

4 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	B4RPP8_NEIG2
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 9–342； UniProt 24–357 Author chain B； PDBConstruct 9–342； UniProt 24–357

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9y4u
Deposition date deposition_date	2025-09-03
最后修订 last_revision	2025-09-17
Structure title title	Crystal structure of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from Neisseria gonorrhoeae in complex with NAD (Orthorhombic I form)
Keywords keywords	SSGCID, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, GAPDH, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	29.25 Å
Radius of gyration Rg (electron density) rg_electron	28.92 Å
Forward intensity I(0) i0	76205900.00
Molecular weight molecular_weight	68202.0 kDa
Excluded volume excluded_volume	85193 Å³
Envelope volume envelope_volume	103270 Å³
Hydration-shell volume shell_volume	31134 Å³
Envelope diameter envelope_diameter	99.2 Å
Shell Rg shell_rg	34.79 Å
Envelope Rg envelope_rg	28.90 Å
Shape Rg shape_rg	28.96 Å
Total Rg total_rg	29.34 Å
Total atoms total_atoms	4787
Residues n_residues	629
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	97.2 Å
Rg (real space) rg_real	29.38 Å
Rg uncertainty (real space) rg_real_error	0.85 Å
I(0) (real space) i0_real	7.6210e+07
I(0) uncertainty (real space) i0_real_error	1.1580e+06
Rg (reciprocal space) rg_reciprocal	29.33 Å
I(0) (reciprocal space) i0_reciprocal	76200000.0000
Solution quality estimate total_estimate	0.8684
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	27.0 Å
Skewness Skewness skewness	0.451
Kurtosis Kurtosis kurtosis	-0.429
Angular range angular_range	— – 0.2700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	45340000.0000
Real-space data points n_real_points	55
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.826; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.920; Smooth: 0.886

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Glyceraldehyde-3-phosphate dehydrogenase
Molecular weight formula_weight	36829.8 kDa
EC 编号 ec_number	1.2.1.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5087

MAHHHHHHMSIKVAINGFGRIGRLALRQIEKAHGIEVAAVNDLTPAEMLLHLFKYDSTQGRFQGTAELKDDAIVVNGREIKVFANPNPEELPWGELGVDVVLECTGFFTNKTKAEAHIRAGARKVVISAPGGNDVKTVVYGVNQDILDGSETVISAASCTTNCLAPMAAVLQKEFGVVEGLMTTIHAYTGDQNTLDAPHRKGDLRRARAAALNIVPNSTGAAKAIGLVIPELNGKLDGSAQRVPVATGSLTELVSVLERPATKEEINAAMKAASSESYGYNEDQIVSSDVVGIEYGSLFDATQTRVMTVGGKQLVKTVAWYDNEMSYTCQLVRTLEYFAGKI

来源 Source

来源生物 organism	Neisseria gonorrhoeae NCCP11945
NCBI Class编号 ncbi_taxonomy_id	521006
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Molecular weight formula_weight	663.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	267

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8. Citations (1)

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Unit-cell length a length_a	87.189 Å
Unit-cell length b length_b	123.985 Å
Unit-cell length c length_c	130.745 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	48.190 Å
R factor r_factor	0.1769
R_work r_work	0.1750
R_free r_free	0.2144

fit	/app/data/saxs_computation/y4/9y4u/9y4u.fit
pddf	/app/data/pr_computation/y4/9y4u/9y4u.pr.out
profile	/app/data/saxs_computation/y4/9y4u/9y4u.dat

Crystal structure of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from Neisseria gonorrhoeae in complex with NAD (Orthorhombic I form)

1. Protein Identity and Related Structures Protein Identity & Related Structures

Glyceraldehyde-3-phosphate dehydrogenase

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction