SAXSdb — 1d2f

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

MALY PROTEIN

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–390 Chain B； UniProt 1–390	Not recorded	PLP PYRIDOXAL-5'-PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；AMMONIUM SULPHATE, MES, TRIS, DITHITHREITOL, pH 7.0, VAPOR DIFFUSION, SITTING DROP	Resolution 2.50 Å R-free 0.262

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 1D2F	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8BOB Structural basis for negative regulation of the maltose system Deposited 2022-11-15	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–390（390 aa） Chain B 1–390（390 aa）	Not recorded	PLP PYRIDOXAL-5'-PHOSPHATE × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.94 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MALY_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–390； UniProt 1–390 Author chain B； PDBConstruct 1–390； UniProt 1–390

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	1d2f
Deposition date deposition_date	1999-09-23
Structure title title	X-RAY STRUCTURE OF MALY FROM ESCHERICHIA COLI: A PYRIDOXAL-5'-PHOSPHATE-DEPENDENT ENZYME ACTING AS A MODULATOR IN MAL GENE EXPRESSION
Keywords keywords	AMINOTRANSFERASE FOLD, LARGE PLP-BINDING DOMAIN, SMALL C-TERMINAL DOMAIN, OPEN ALPHA-BETA STRUCTURE., TRANSFERASE; TRANSFERASE
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	29.07 Å
Radius of gyration Rg (electron density) rg_electron	28.30 Å
Forward intensity I(0) i0	104531000.00
Molecular weight molecular_weight	81675.0 kDa
Excluded volume excluded_volume	102470 Å³
Envelope volume envelope_volume	121590 Å³
Hydration-shell volume shell_volume	36028 Å³
Envelope diameter envelope_diameter	99.6 Å
Shell Rg shell_rg	35.76 Å
Envelope Rg envelope_rg	28.31 Å
Shape Rg shape_rg	28.29 Å
Total Rg total_rg	29.03 Å
Total atoms total_atoms	5747
Residues n_residues	729
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	96.0 Å
Rg (real space) rg_real	29.08 Å
Rg uncertainty (real space) rg_real_error	0.68 Å
I(0) (real space) i0_real	1.0450e+08
I(0) uncertainty (real space) i0_real_error	1.6130e+06
Rg (reciprocal space) rg_reciprocal	29.08 Å
I(0) (reciprocal space) i0_reciprocal	104500000.0000
Solution quality estimate total_estimate	0.8851
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	33.2 Å
Skewness Skewness skewness	0.398
Kurtosis Kurtosis kurtosis	-0.252
Angular range angular_range	— – 0.2750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	54780000.0000
Real-space data points n_real_points	56
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.862; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.972; Smooth: 0.945

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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	MALY PROTEIN
Molecular weight formula_weight	43684.7 kDa
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	5914

MFDFSKVVDRHGTWCTQWDYVADRFGTADLLPFTISDMDFATAPCIIEALNQRLMHGVFGYSRWKNDEFLAAIAHWFSTQHYTAIDSQTVVYGPSVIYMVSELIRQWSETGEGVVIHTPAYDAFYKAIEGNQRTVMPVALEKQADGWFCDMGKLEAVLAKPECKIMLLCSPQNPTGKVWTCDELEIMADLCERHGVRVISDEIHMDMVWGEQPHIPWSNVARGDWALLTSGSKSFNIPALTGAYGIIENSSSRDAYLSALKGRDGLSSPSVLALTAHIAAYQQGAPWLDALRIYLKDNLTYIADKMNAAFPELNWQIPQSTYLAWLDLRPLNIDDNALQKALIEQEKVAIMPGYTYGEEGRGFVRLNAGCPRSKLEKGVAGLINAIRAVR

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	PYRIDOXAL-5'-PHOSPHATE
Molecular weight formula_weight	247.1 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	167

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1d2fa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.67 — PLP-dependent transferase-like
Superfamily Superfamily superfamily	c.67.1 — PLP-dependent transferases
Family Family family	c.67.1.3 — Cystathionine synthase-like

Domain ID domain_id	d1d2fb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.67 — PLP-dependent transferase-like
Superfamily Superfamily superfamily	c.67.1 — PLP-dependent transferases
Family Family family	c.67.1.3 — Cystathionine synthase-like

CATH v4.4 (4 domains)

Domain ID domain_id	1d2fA01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	10 — Aspartate Aminotransferase, domain 1

Domain ID domain_id	1d2fA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

Domain ID domain_id	1d2fB01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	10 — Aspartate Aminotransferase, domain 1

Domain ID domain_id	1d2fB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

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8. Citations (2)

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Unit-cell length a length_a	57.510 Å
Unit-cell length b length_b	107.190 Å
Unit-cell length c length_c	256.400 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2040
R_work r_work	0.2010
R_free r_free	0.2620

fit	/app/data/saxs_computation/d2/1d2f/1d2f.fit
pddf	/app/data/pr_computation/d2/1d2f/1d2f.pr.out
profile	/app/data/saxs_computation/d2/1d2f/1d2f.dat

X-RAY STRUCTURE OF MALY FROM ESCHERICHIA COLI: A PYRIDOXAL-5'-PHOSPHATE-DEPENDENT ENZYME ACTING AS A MODULATOR IN MAL GENE EXPRESSION

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

MALY PROTEIN

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