SAXSdb — 1p7t

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

Malate synthase G

Escherichia coli str. K12 substr.

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, 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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–722	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

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 1P7T	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 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
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 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MASZ_ECOLI
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 2–723； UniProt 1–722 Author chain B； 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1p7t
Deposition date deposition_date	2003-05-05
Structure title title	Structure of Escherichia coli malate synthase G:pyruvate:acetyl-Coenzyme A abortive ternary complex at 1.95 angstrom resolution
Keywords keywords	TIM barrel, Glyoxylate cycle, Acetyl-COA, cysteine-sulfenic acid, 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	39.12 Å
Radius of gyration Rg (electron density) rg_electron	39.09 Å
Forward intensity I(0) i0	375697000.00
Molecular weight molecular_weight	155390.0 kDa
Excluded volume excluded_volume	193170 Å³
Envelope volume envelope_volume	237080 Å³
Hydration-shell volume shell_volume	51393 Å³
Envelope diameter envelope_diameter	142.9 Å
Shell Rg shell_rg	43.89 Å
Envelope Rg envelope_rg	39.24 Å
Shape Rg shape_rg	39.12 Å
Total Rg total_rg	39.22 Å
Total atoms total_atoms	10921
Residues n_residues	1408
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	136.0 Å
Rg (real space) rg_real	39.41 Å
Rg uncertainty (real space) rg_real_error	1.18 Å
I(0) (real space) i0_real	3.7570e+08
I(0) uncertainty (real space) i0_real_error	5.6650e+06
Rg (reciprocal space) rg_reciprocal	39.24 Å
I(0) (reciprocal space) i0_reciprocal	375600000.0000
Solution quality estimate total_estimate	0.6187
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	37.4 Å
Skewness Skewness skewness	0.504
Kurtosis Kurtosis kurtosis	-0.266
Angular range angular_range	— – 0.2000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	87390000.0000
Real-space data points n_real_points	41
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.774; Stabil: 1.000; Sysdev: 0.013; Positv: 1.000; Valcen: 0.873; Smooth: 0.805

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	Malate synthase G
Molecular weight formula_weight	81652.5 kDa
EC 编号 ec_number	2.3.3.9
Mutation mutation	S2A, C-terminal LEHHHHHH tag
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	11504

MAQTITQSRLRIDANFKRFVDEEVLPGTGLDAAAFWRNFDEIVHDLAPENRQLLAERDRIQAALDEWHRSNPGPVKDKAAYKSFLRELGYLVPQPERVTVETTGIDSEITSQAGPQLVVPAMNARYALNAANARWGSLYDALYGSDIIPQEGAMVSGYDPQRGEQVIAWVRRFLDESLPLENGSYQDVVAFKVVDKQLRIQLKNGKETTLRTPAQFVGYRGDAAAPTCILLKNNGLHIELQIDANGRIGKDDPAHINDVIVEAAISTILDCEDSVAAVDAEDKILLYRNLLGLMQGTLQEKMEKNGRQIVRKLNDDRHYTAADGSEISLHGRSLLFIRNVGHLMTIPVIWDSEGNEIPEGILDGVMTGAIALYDLKVQKNSRTGSVYIVKPKMHGPQEVAFANKLFTRIETMLGMAPNTLKMGIMDEERRTSLNLRSCIAQARNRVAFINTGFLDRTGDEMHSVMEAGPMLRKNQMKSTPWIKAYERNNVLSGLFCGLRGKAQIGKGMWAMPDLMADMYSQKGDQLRAGANTAWVPSPTAATLHALHYHQTNVQSVQANIAQTEFNAEFEPLLDDLLTIPVAENANWSAQEIQQELDNNVQGILGYVVRWVEQGIGCSKVPDIHNVALMEDRATLRISSQHIANWLRHGILTKEQVQASLENMAKVVDQQNAGDPAYRPMAGNFANSCAFKAASDLIFLGVKQPNGYTEPLLHAWRLREKESHLEHHHHHH

来源 Source

来源生物 organism	Escherichia coli str. K12 substr.
NCBI Class编号 ncbi_taxonomy_id	316407
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Malate synthase G
Molecular weight formula_weight	81668.5 kDa
EC 编号 ec_number	2.3.3.9
Mutation mutation	S2A, C-terminal LEHHHHHH tag
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MAQTITQSRLRIDANFKRFVDEEVLPGTGLDAAAFWRNFDEIVHDLAPENRQLLAERDRIQAALDEWHRSNPGPVKDKAAYKSFLRELGYLVPQPERVTVETTGIDSEITSQAGPQLVVPAMNARYALNAANARWGSLYDALYGSDIIPQEGAMVSGYDPQRGEQVIAWVRRFLDESLPLENGSYQDVVAFKVVDKQLRIQLKNGKETTLRTPAQFVGYRGDAAAPTCILLKNNGLHIELQIDANGRIGKDDPAHINDVIVEAAISTILDCEDSVAAVDAEDKILLYRNLLGLMQGTLQEKMEKNGRQIVRKLNDDRHYTAADGSEISLHGRSLLFIRNVGHLMTIPVIWDSEGNEIPEGILDGVMTGAIALYDLKVQKNSRTGSVYIVKPKMHGPQEVAFANKLFTRIETMLGMAPNTLKMGIMDEERRTSLNLRSCIAQARNRVAFINTGFLDRTGDEMHSVMEAGPMLRKNQMKSTPWIKAYERNNVLSGLFCGLRGKAQIGKGMWAMPDLMADMYSQKGDQLRAGANTAWVPSPTAATLHALHYHQTNVQSVQANIAQTEFNAEFEPLLDDLLTIPVAENANWSAQEIQQELDNNVQGILGYVVRWVEQGIGCSKVPDIHNVALMEDRATLRISSQHIANWLRHGILTKEQVQASLENMAKVVDQQNAGDPAYRPMAGNFANSCAFKAASDLIFLGVKQPNGYTEPLLHAWRLREKESHLEHHHHHH

来源 Source

来源生物 organism	Escherichia coli str. K12 substr.
NCBI Class编号 ncbi_taxonomy_id	316407
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	ACETYL COENZYME *A
Molecular weight formula_weight	809.6 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	PYRUVIC ACID
Molecular weight formula_weight	88.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	TETRAETHYLENE GLYCOL
Molecular weight formula_weight	194.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	583

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1p7ta_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.13 — Malate synthase G
Family Family family	c.1.13.1 — Malate synthase G

Domain ID domain_id	d1p7tb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.13 — Malate synthase G
Family Family family	c.1.13.1 — Malate synthase G

CATH v4.4 (6 domains)

Domain ID domain_id	1p7tA01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	360 — Malate synthase, domain 3

Domain ID domain_id	1p7tA02
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	170 — Malate synthase G - maily-beta sub-domain
Homologous superfamily homologous superfamily	11 — Malate synthase G - maily-beta sub-domain

Domain ID domain_id	1p7tA03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1220 — Malate Synthase G; Chain: A; Domain 4
Homologous superfamily homologous superfamily	12 — Malate synthase, domain III

Domain ID domain_id	1p7tB01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	360 — Malate synthase, domain 3

Domain ID domain_id	1p7tB02
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	170 — Malate synthase G - maily-beta sub-domain
Homologous superfamily homologous superfamily	11 — Malate synthase G - maily-beta sub-domain

Domain ID domain_id	1p7tB03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1220 — Malate Synthase G; Chain: A; Domain 4
Homologous superfamily homologous superfamily	12 — Malate synthase, domain III

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8. Citations (1)

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Unit-cell length a length_a	73.931 Å
Unit-cell length b length_b	107.394 Å
Unit-cell length c length_c	204.974 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	4

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

Resolution resolution	1.950 Å
Low-resolution limit resolution_low	39.220 Å
R factor r_factor	0.1970
R_work r_work	0.1940
R_free r_free	0.2940

fit	/app/data/saxs_computation/p7/1p7t/1p7t.fit
pddf	/app/data/pr_computation/p7/1p7t/1p7t.pr.out
profile	/app/data/saxs_computation/p7/1p7t/1p7t.dat

Structure of Escherichia coli malate synthase G:pyruvate:acetyl-Coenzyme A abortive ternary complex at 1.95 angstrom resolution

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

Malate synthase G

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

6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

CATH v4.4 (6 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)