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7yqn

Crystal structure of Ecoli malate synthase G

Method: X-RAY DIFFRACTION Dmax: 124.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Malate synthase G

Escherichia coli DH5[alpha]

UniProt P37330

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 1–723 Not recorded CL CHLORIDE ION × 2 NA SODIUM ION × 1 BME BETA-MERCAPTOETHANOL × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；295 K；19-22% PEG4000, 0.2M NaCl, 0.1M Tris pH 7.6-8.5 Resolution 1.60 Å R-free 0.172
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 1–723 Not recorded CL CHLORIDE ION × 1 NA SODIUM ION × 1 BME BETA-MERCAPTOETHANOL × 1 GOL GLYCEROL × 3 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；295 K；19-22% PEG4000, 0.2M NaCl, 0.1M Tris pH 7.6-8.5 Resolution 1.60 Å R-free 0.172

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 7YQN Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1D8C MALATE SYNTHASE G COMPLEXED WITH MAGNESIUM AND GLYOXYLATE Deposited 1999-10-22 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–722（722 aa）
Mutation：S2A Non-standard monomer：Yes (specific site not provided by mmCIF) SOR sorbitol × 1 MG MAGNESIUM ION × 1 SO4 SULFATE ION × 5 GLV GLYOXYLIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；ammonium sulfate, sorbitol, imidazole, magnesium, DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.00 Å
1P7T Structure of Escherichia coli malate synthase G:pyruvate:acetyl-Coenzyme A abortive ternary complex at 1.95 angstrom resolution Deposited 2003-05-05 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–722（722 aa）
Mutation：S2A, C-terminal LEHHHHHH tag Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 1 ACO ACETYL COENZYME *A × 1 PYR PYRUVIC ACID × 1 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.9；298 K；MgCl2, Tris, DTT, pyruvate, acetyl-Coenzyme A, HEPES, PEG-8000, sodium acetate, pH 7.9, VAPOR DIFFUSION, temperature 298K
Resolution 1.95 Å R-free 0.294
1P7T Structure of Escherichia coli malate synthase G:pyruvate:acetyl-Coenzyme A abortive ternary complex at 1.95 angstrom resolution Deposited 2003-05-05 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–722（722 aa）
Mutation：S2A, C-terminal LEHHHHHH tag Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 1 ACO ACETYL COENZYME *A × 1 PYR PYRUVIC ACID × 1 PG4 TETRAETHYLENE GLYCOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.9；298 K；MgCl2, Tris, DTT, pyruvate, acetyl-Coenzyme A, HEPES, PEG-8000, sodium acetate, pH 7.9, VAPOR DIFFUSION, temperature 298K
Resolution 1.95 Å R-free 0.294
1Y8B Solution NMR-Derived Global Fold of Malate Synthase G from E.coli Deposited 2004-12-10 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 1–722（722 aa）
Mutation：S2A No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.1；310 K；Ionic strength (raw mmCIF value) 25 mM sodium phosphate; 20 mM Magnesium Chloride；Pressure ambient
Resolution not provided
2JQX Solution structure of Malate Synthase G from joint refinement against NMR and SAXS data Deposited 2007-06-13 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 1–723（723 aa）
Mutation：S2A No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.1；293 K；Ionic strength (raw mmCIF value) 170；Pressure ambient
NMR sample composition 0.17 mM [U-100% 15N], Ile CD1-[13CH3] MALATE SYNTHASE G, 20 mM sodium phosphate, 5 mM DTT, 150 mM sodium chloride, 100% H2O | 100% H2O
Resolution not provided
7YQM 2.9-angstrom cryo-EM structure of Ecoli malate synthase G Deposited 2022-08-08 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 1–723（723 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.89 Å

5 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MASZ_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–723； UniProt 1–723 Author chain B； PDBConstruct 1–723； UniProt 1–723

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 7yqn

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7yqn
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7yqn
Deposition date deposition_date2022-08-08
Structure title titleCrystal structure of Ecoli malate synthase G
Keywords keywordsglyoxylate, malate, MSG, citric acid cycel, malate synthase G, BIOSYNTHETIC PROTEIN; BIOSYNTHETIC PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier37.95 Å
Radius of gyration Rg (electron density) rg_electron37.36 Å
Forward intensity I(0) i0396311000.00
Molecular weight molecular_weight159210.0 kDa
Excluded volume excluded_volume198100 ų
Envelope volume envelope_volume248170 ų
Hydration-shell volume shell_volume54410 ų
Envelope diameter envelope_diameter127.7 Å
Shell Rg shell_rg44.33 Å
Envelope Rg envelope_rg37.06 Å
Shape Rg shape_rg37.37 Å
Total Rg total_rg37.73 Å
Total atoms total_atoms11177
Residues n_residues1429
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 dmax124.2 Å
Rg (real space) rg_real37.89 Å
Rg uncertainty (real space) rg_real_error1.23 Å
I(0) (real space) i0_real3.9630e+08
I(0) uncertainty (real space) i0_real_error6.9140e+06
Rg (reciprocal space) rg_reciprocal37.93 Å
I(0) (reciprocal space) i0_reciprocal396300000.0000
Solution quality estimate total_estimate0.8966
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary44.4 Å
Skewness Skewness skewness0.265
Kurtosis Kurtosis kurtosis-0.517
Angular range angular_range— – 0.2100 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha67110000.0000
Real-space data points n_real_points43
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.911; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.918
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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8. Citations (1)

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9. Files and Curves (10)