SAXSdb — 8bob

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

Protein MalY

Escherichia coli K-12

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–390 Chain B； UniProt 1–390	Not recorded	HTH-type transcriptional regulator MalT × 2 （B1X764） 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

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 8BOB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1D2F X-RAY STRUCTURE OF MALY FROM ESCHERICHIA COLI: A PYRIDOXAL-5'-PHOSPHATE-DEPENDENT ENZYME ACTING AS A MODULATOR IN MAL GENE EXPRESSION Deposited 1999-09-23	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–390（390 aa） Chain B 1–390（390 aa）	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

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

HTH-type transcriptional regulator MalT

Escherichia coli

UniProt B1X764

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain C； UniProt 1–409 Chain D； UniProt 1–409	Not recorded	Protein MalY × 2 （P23256） 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

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	MALT_ECODH
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–409； UniProt 1–409 Author chain D； PDBConstruct 1–409； UniProt 1–409

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	8bob
Deposition date deposition_date	2022-11-15
Structure title title	Structural basis for negative regulation of the maltose system
Keywords keywords	STAND, maltose system, transcription, oligomerization; TRANSCRIPTION
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	42.57 Å
Radius of gyration Rg (electron density) rg_electron	42.10 Å
Forward intensity I(0) i0	493794000.00
Molecular weight molecular_weight	180570.0 kDa
Excluded volume excluded_volume	225350 Å³
Envelope volume envelope_volume	310880 Å³
Hydration-shell volume shell_volume	63243 Å³
Envelope diameter envelope_diameter	143.2 Å
Shell Rg shell_rg	45.90 Å
Envelope Rg envelope_rg	41.29 Å
Shape Rg shape_rg	42.09 Å
Total Rg total_rg	42.33 Å
Total atoms total_atoms	12712
Residues n_residues	1604
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	144.7 Å
Rg (real space) rg_real	42.70 Å
Rg uncertainty (real space) rg_real_error	1.53 Å
I(0) (real space) i0_real	4.9380e+08
I(0) uncertainty (real space) i0_real_error	8.4720e+06
Rg (reciprocal space) rg_reciprocal	42.57 Å
I(0) (reciprocal space) i0_reciprocal	493700000.0000
Solution quality estimate total_estimate	0.8542
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	50.8 Å
Skewness Skewness skewness	0.454
Kurtosis Kurtosis kurtosis	-0.267
Angular range angular_range	— – 0.1850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	88040000.0000
Real-space data points n_real_points	38
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.748; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.874

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Protein MalY
Molecular weight formula_weight	43684.7 kDa
EC 编号 ec_number	4.4.1.13
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	12712

MFDFSKVVDRHGTWCTQWDYVADRFGTADLLPFTISDMDFATAPCIIEALNQRLMHGVFGYSRWKNDEFLAAIAHWFSTQHYTAIDSQTVVYGPSVIYMVSELIRQWSETGEGVVIHTPAYDAFYKAIEGNQRTVMPVALEKQADGWFCDMGKLEAVLAKPECKIMLLCSPQNPTGKVWTCDELEIMADLCERHGVRVISDEIHMDMVWGEQPHIPWSNVARGDWALLTSGSKSFNIPALTGAYGIIENSSSRDAYLSALKGRDGLSSPSVLALTAHIAAYQQGAPWLDALRIYLKDNLTYIADKMNAAFPELNWQIPQSTYLAWLDLRPLNIDDNALQKALIEQEKVAIMPGYTYGEEGRGFVRLNAGCPRSKLEKGVAGLINAIRAVR

来源 Source

来源生物 organism	Escherichia coli K-12
NCBI Class编号 ncbi_taxonomy_id	83333
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	HTH-type transcriptional regulator MalT
Molecular weight formula_weight	47318.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

MLIPSKLSRPVRLDHTVVRERLLAKLSGANNFRLALITSPAGYGKTTLISQWAAGKNDIGWYSLDEGDNQQERFASYLIAAVQQATNGHCAICETMAQKRQYASLTSLFAQLFIELAEWHSPLYLVIDDYHLITNPVIHESMRFFIRHQPENLTLVVLSRNLPQLGIANLRVRDQLLEIGSQQLAFTHQEANEFFDCRLSSPIEAAESSRICDDVSGWATALQLIALSARQNTHSAHKSARRLAGINASHLSDYLVDEVLDNVDLATRHFLLKSAILRSMNDALITRVTGEENGQMRLEEIERQGLFLQRMDDTGEWFCYHPLFGNFLRQRCQWELAAELPEIHRAAAESWMAQGFPSEAIHHALAAGDALMLRDILLNHAWSLFNHSELSLLEESLKALPWDSLLENPAAAIAIAIIEV

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 3 Entity 3 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 4 Entity 4 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	2

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.94 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	176969

fit	/app/data/saxs_computation/bo/8bob/8bob.fit
pddf	/app/data/pr_computation/bo/8bob/8bob.pr.out
profile	/app/data/saxs_computation/bo/8bob/8bob.dat

Structural basis for negative regulation of the maltose system

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

Protein MalY

State in the Current Structure

Other States of the Same Protein in the Database

HTH-type transcriptional regulator MalT

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (4)

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

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)