SAXSdb — 1s89

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

Methylglyoxal synthase

Escherichia coli

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 × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 1–152 Chain B； UniProt 1–152 Chain C； UniProt 1–152 Chain D； UniProt 1–152 Chain E； UniProt 1–152 Chain F； UniProt 1–152	Mutation：H98N	PGA 2-PHOSPHOGLYCOLIC ACID × 6	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.2；298 K；PEG 1500, Sodium Cacodylate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.22 Å R-free 0.229

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 1S89	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B93 METHYLGLYOXAL SYNTHASE FROM ESCHERICHIA COLI Deposited 1999-02-23	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–152（152 aa） Chain B 1–152（152 aa） Chain C 1–152（152 aa）	Not recorded	FMT FORMIC ACID × 14 PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 1.90 Å R-free 0.202
1EGH STRUCTURE OF METHYLGLYOXAL SYNTHASE COMPLEXED WITH THE COMPETITIVE INHIBITOR 2-PHOSPHOGLYCOLATE Deposited 2000-02-15	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–152（152 aa） Chain B 1–152（152 aa） Chain C 1–152（152 aa） Chain D 1–152（152 aa） Chain E 1–152（152 aa） Chain F 1–152（152 aa）	Not recorded	PGA 2-PHOSPHOGLYCOLIC ACID × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；PEG 1500, sodium cacodylate, imidazole-HCL, potassium phosphate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.00 Å R-free 0.219
1IK4 X-ray Structure of Methylglyoxal Synthase from E. coli Complexed with Phosphoglycolohydroxamic Acid Deposited 2001-05-02	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–152（152 aa） Chain B 1–152（152 aa） Chain C 1–152（152 aa） Chain D 1–152（152 aa） Chain E 1–152（152 aa） Chain F 1–152（152 aa）	Not recorded	PGH PHOSPHOGLYCOLOHYDROXAMIC ACID × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；PEG 1500, Sodium Cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.00 Å R-free 0.206
1S8A H98Q Mutant of Methylglyoxal Synthase from E. coli complexed with Phosphoglycolic Acid Deposited 2004-01-31	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–152（152 aa） Chain B 1–152（152 aa） Chain C 1–152（152 aa） Chain D 1–152（152 aa） Chain E 1–152（152 aa） Chain F 1–152（152 aa）	Mutation：H98Q Mutation：H98Q Mutation：H98Q Mutation：H98Q Mutation：H98Q Mutation：H98Q	PGA 2-PHOSPHOGLYCOLIC ACID × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；PEG 1500, Sodium Cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.20 Å R-free 0.227

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

View Construct and Data Evidence

UniProt name	MGSA_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–152； UniProt 1–152 Author chain B； PDBConstruct 1–152； UniProt 1–152 Author chain C； PDBConstruct 1–152； UniProt 1–152 Author chain D； PDBConstruct 1–152； UniProt 1–152 Author chain E； PDBConstruct 1–152； UniProt 1–152 Author chain F； PDBConstruct 1–152； UniProt 1–152

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	1s89
Deposition date deposition_date	2004-01-31
Structure title title	H98N Mutant of Methylglyoxal Synthase from E. coli complexed with Phosphoglycolic Acid
Keywords keywords	GLYCOLYTIC BYPASS, METHYLGLYOXAL, LYASE; LYASE
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	29.00 Å
Radius of gyration Rg (electron density) rg_electron	27.77 Å
Forward intensity I(0) i0	159780000.00
Molecular weight molecular_weight	100790.0 kDa
Excluded volume excluded_volume	126490 Å³
Envelope volume envelope_volume	148800 Å³
Hydration-shell volume shell_volume	42660 Å³
Envelope diameter envelope_diameter	86.0 Å
Shell Rg shell_rg	36.89 Å
Envelope Rg envelope_rg	27.58 Å
Shape Rg shape_rg	27.78 Å
Total Rg total_rg	28.59 Å
Total atoms total_atoms	7082
Residues n_residues	912
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	86.3 Å
Rg (real space) rg_real	28.82 Å
Rg uncertainty (real space) rg_real_error	0.53 Å
I(0) (real space) i0_real	1.5980e+08
I(0) uncertainty (real space) i0_real_error	2.3570e+06
Rg (reciprocal space) rg_reciprocal	28.90 Å
I(0) (reciprocal space) i0_reciprocal	159800000.0000
Solution quality estimate total_estimate	0.9086
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	36.1 Å
Skewness Skewness skewness	0.085
Kurtosis Kurtosis kurtosis	-0.587
Angular range angular_range	— – 0.2750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	36000000.0000
Real-space data points n_real_points	56
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.956; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.959

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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	Methylglyoxal synthase
Molecular weight formula_weight	16913.5 kDa
EC 编号 ec_number	4.2.3.3
Mutation mutation	H98N
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	7210

MELTTRTLPARKHIALVAHDHCKQMLMSWVERHQPLLEQHVLYATGTTGNLISRATGMNVNAMLSGPMGGDQQVGALISEGKIDVLIFFWDPLNAVPNDPDVKALLRLATVWNIPVATNVATADFIIQSPHFNDAVDILIPDYQRYLADRLK

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	2-PHOSPHOGLYCOLIC ACID
Molecular weight formula_weight	156.0 kDa
Source method src_method	man
Copy count entity_count	6

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	128

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1s89a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.24 — Methylglyoxal synthase-like
Superfamily Superfamily superfamily	c.24.1 — Methylglyoxal synthase-like
Family Family family	c.24.1.2 — Methylglyoxal synthase, MgsA

Domain ID domain_id	d1s89b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.24 — Methylglyoxal synthase-like
Superfamily Superfamily superfamily	c.24.1 — Methylglyoxal synthase-like
Family Family family	c.24.1.2 — Methylglyoxal synthase, MgsA

Domain ID domain_id	d1s89c_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.24 — Methylglyoxal synthase-like
Superfamily Superfamily superfamily	c.24.1 — Methylglyoxal synthase-like
Family Family family	c.24.1.2 — Methylglyoxal synthase, MgsA

Domain ID domain_id	d1s89d_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.24 — Methylglyoxal synthase-like
Superfamily Superfamily superfamily	c.24.1 — Methylglyoxal synthase-like
Family Family family	c.24.1.2 — Methylglyoxal synthase, MgsA

Domain ID domain_id	d1s89e_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.24 — Methylglyoxal synthase-like
Superfamily Superfamily superfamily	c.24.1 — Methylglyoxal synthase-like
Family Family family	c.24.1.2 — Methylglyoxal synthase, MgsA

Domain ID domain_id	d1s89f_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.24 — Methylglyoxal synthase-like
Superfamily Superfamily superfamily	c.24.1 — Methylglyoxal synthase-like
Family Family family	c.24.1.2 — Methylglyoxal synthase, MgsA

CATH v4.4 (6 domains)

Domain ID domain_id	1s89A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1380 — Methylglyoxal synthase-like domain

Domain ID domain_id	1s89B00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1380 — Methylglyoxal synthase-like domain

Domain ID domain_id	1s89C00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1380 — Methylglyoxal synthase-like domain

Domain ID domain_id	1s89D00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1380 — Methylglyoxal synthase-like domain

Domain ID domain_id	1s89E00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1380 — Methylglyoxal synthase-like domain

Domain ID domain_id	1s89F00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1380 — Methylglyoxal synthase-like domain

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8. Citations (1)

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Unit-cell length a length_a	53.479 Å
Unit-cell length b length_b	129.497 Å
Unit-cell length c length_c	178.220 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	24

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.220 Å
Low-resolution limit resolution_low	29.240 Å
R factor r_factor	—
R_work r_work	0.1900
R_free r_free	0.2290

fit	/app/data/saxs_computation/s8/1s89/1s89.fit
pddf	/app/data/pr_computation/s8/1s89/1s89.pr.out
profile	/app/data/saxs_computation/s8/1s89/1s89.dat

H98N Mutant of Methylglyoxal Synthase from E. coli complexed with Phosphoglycolic Acid

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

Methylglyoxal synthase

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