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1d8c

MALATE SYNTHASE G COMPLEXED WITH MAGNESIUM AND GLYOXYLATE

Method: X-RAY DIFFRACTION Dmax: 82.9 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

MALATE SYNTHASE G

Escherichia coli

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 1–722 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

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 1D8C Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
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 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 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 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 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 1–723（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 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 1–723（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
7YQN Crystal structure of Ecoli malate synthase G Deposited 2022-08-08 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 1–723（723 aa）
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
7YQN Crystal structure of Ecoli malate synthase G Deposited 2022-08-08 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 1–723（723 aa）
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

5 other PDB entries and 7 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 2–723； UniProt 1–722

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 1d8c

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1d8c
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1d8c
Deposition date deposition_date1999-10-22
Structure title titleMALATE SYNTHASE G COMPLEXED WITH MAGNESIUM AND GLYOXYLATE
Keywords keywordsALPHA-BETA BARREL, TIM BARREL, GLYOXYLATE CYCLE, ENOLIZATION, CONDENSATION, CONCERTED ACID-BASE CATALYSIS, LYASE; LYASE
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_guinier27.00 Å
Radius of gyration Rg (electron density) rg_electron26.08 Å
Forward intensity I(0) i0104929000.00
Molecular weight molecular_weight77468.0 kDa
Excluded volume excluded_volume95188 ų
Envelope volume envelope_volume111640 ų
Hydration-shell volume shell_volume34996 ų
Envelope diameter envelope_diameter88.2 Å
Shell Rg shell_rg34.11 Å
Envelope Rg envelope_rg26.33 Å
Shape Rg shape_rg26.16 Å
Total Rg total_rg26.59 Å
Total atoms total_atoms5374
Residues n_residues688
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 dmax82.9 Å
Rg (real space) rg_real26.90 Å
Rg uncertainty (real space) rg_real_error0.44 Å
I(0) (real space) i0_real1.0490e+08
I(0) uncertainty (real space) i0_real_error1.5360e+06
Rg (reciprocal space) rg_reciprocal26.93 Å
I(0) (reciprocal space) i0_reciprocal104900000.0000
Solution quality estimate total_estimate0.9056
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary32.3 Å
Skewness Skewness skewness0.251
Kurtosis Kurtosis kurtosis-0.425
Angular range angular_range— – 0.2950 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha26300000.0000
Real-space data points n_real_points60
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.943; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.940
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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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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1d8ca_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.13 — Malate synthase G
Family Family familyc.1.13.1 — Malate synthase G

CATH v4.4 (3 domains)

Domain ID domain_id1d8cA01
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily360 — Malate synthase, domain 3
Domain ID domain_id1d8cA02
Class class2 — Mainly Beta
Architecture architecture170 — Beta Complex
Topology topology170 — Malate synthase G - maily-beta sub-domain
Homologous superfamily homologous superfamily11 — Malate synthase G - maily-beta sub-domain
Domain ID domain_id1d8cA03
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1220 — Malate Synthase G; Chain: A; Domain 4
Homologous superfamily homologous superfamily12 — Malate synthase, domain III
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8. Citations (1)

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9. Files and Curves (10)