SAXSdb — 8hqa

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

Intermembrane phospholipid transport system binding protein MlaD

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 homooligomer Homooligomer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 29–183 Chain B； UniProt 29–183 Chain C； UniProt 29–183	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：MICROBATCH；pH 8.5；293 K；0.01 M nickel(II) chloride hexahydrate, 0.1 M tris pH 8.5, 20% (w/v) PEG monoethyl ether 2000	Resolution 3.20 Å R-free 0.275

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 8HQA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8HPZ Crystal structure of the MlaD domain of the MlaD protein from Escherichia coli (Form I) Deposited 2022-12-13	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 29–183（155 aa） Chain B 29–183（155 aa） Chain C 29–183（155 aa）	Not recorded	CO2 CARBON DIOXIDE × 2 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH；pH 5；293 K；1.8 M sodium phosphate monobasic monohydrate, potassium phosphate dibasic pH 5.0	Resolution 2.30 Å R-free 0.273
8HQ9 Crystal structure of the MlaD domain of the MlaD protein from Escherichia coli (Form II) Deposited 2022-12-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 29–183（155 aa） Chain B 29–183（155 aa） Chain C 29–183（155 aa） Chain D 29–183（155 aa） Chain E 29–183（155 aa） Chain F 29–183（155 aa）	Not recorded	MG MAGNESIUM ION × 1 CO2 CARBON DIOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH；pH 5；293 K；0.2 M magnesium chloride hexahydrate, 0.1 M sodium citrate tribasic dihyrate pH 5.0, 10% (w/v) PEG 20000	Resolution 2.70 Å R-free 0.261
8OJ4 Structure of the MlaCD complex (1:6 stoichiometry) Deposited 2023-03-23	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain A 1–183（183 aa） Chain B 1–183（183 aa） Chain C 1–183（183 aa） Chain D 1–183（183 aa） Chain E 1–183（183 aa） Chain F 1–183（183 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.35 Å
8OJG Structure of the MlaCD complex (2:6 stoichiometry) Deposited 2023-03-24	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–183（183 aa） Chain B 1–183（183 aa） Chain C 1–183（183 aa） Chain D 1–183（183 aa） Chain E 1–183（183 aa） Chain F 1–183（183 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.38 Å

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MLAD_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 8–162； UniProt 29–183 Author chain B； PDBConstruct 8–162； UniProt 29–183 Author chain C； PDBConstruct 8–162； UniProt 29–183

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	8hqa
Deposition date deposition_date	2022-12-13
Structure title title	Crystal structure of the ectodomain of the MlaD protein from Escherichia coli in the resting state
Keywords keywords	ABC transporter, Asymmetric protomer movement, Central channel, Gram-negative bacteria, Mla system, Transport, TRANSPORT PROTEIN; TRANSPORT PROTEIN
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	24.01 Å
Radius of gyration Rg (electron density) rg_electron	23.58 Å
Forward intensity I(0) i0	23188100.00
Molecular weight molecular_weight	37479.0 kDa
Excluded volume excluded_volume	47380 Å³
Envelope volume envelope_volume	61714 Å³
Hydration-shell volume shell_volume	22595 Å³
Envelope diameter envelope_diameter	88.3 Å
Shell Rg shell_rg	29.44 Å
Envelope Rg envelope_rg	23.95 Å
Shape Rg shape_rg	23.60 Å
Total Rg total_rg	24.33 Å
Total atoms total_atoms	2645
Residues n_residues	343
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	81.6 Å
Rg (real space) rg_real	24.02 Å
Rg uncertainty (real space) rg_real_error	0.75 Å
I(0) (real space) i0_real	2.3190e+07
I(0) uncertainty (real space) i0_real_error	3.3600e+05
Rg (reciprocal space) rg_reciprocal	24.02 Å
I(0) (reciprocal space) i0_reciprocal	23190000.0000
Solution quality estimate total_estimate	0.5914
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	26.8 Å
Skewness Skewness skewness	0.356
Kurtosis Kurtosis kurtosis	-0.239
Angular range angular_range	— – 0.3300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5770000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.812; Stabil: 0.996; Sysdev: 0.101; Positv: 1.000; Valcen: 0.959; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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Unit-cell length a length_a	64.280 Å
Unit-cell length b length_b	64.280 Å
Unit-cell length c length_c	231.060 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	24

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	3.200 Å
Low-resolution limit resolution_low	61.930 Å
R factor r_factor	0.2101
R_work r_work	0.2064
R_free r_free	0.2754

Description description	Intermembrane phospholipid transport system binding protein MlaD
Molecular weight formula_weight	17462.3 kDa
Source method src_method	man
Copy count entity_count	3

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	2673

Crystal structure of the ectodomain of the MlaD protein from Escherichia coli in the resting state

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

Intermembrane phospholipid transport system binding protein MlaD

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	22

fit	/app/data/saxs_computation/hq/8hqa/8hqa.fit
pddf	/app/data/pr_computation/hq/8hqa/8hqa.pr.out
profile	/app/data/saxs_computation/hq/8hqa/8hqa.dat