SAXSdb — 8hpz

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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	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

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 8HPZ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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
8HQA Crystal structure of the ectodomain of the MlaD protein from Escherichia coli in the resting state 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	No recorded non-water small molecule	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
8OJ4 Structure of the MlaCD complex (1:6 stoichiometry) Deposited 2023-03-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion 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 ligand/ion 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	8hpz
Deposition date deposition_date	2022-12-13
Structure title title	Crystal structure of the MlaD domain of the MlaD protein from Escherichia coli (Form I)
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	21.99 Å
Radius of gyration Rg (electron density) rg_electron	21.15 Å
Forward intensity I(0) i0	19985000.00
Molecular weight molecular_weight	34153.0 kDa
Excluded volume excluded_volume	42966 Å³
Envelope volume envelope_volume	53995 Å³
Hydration-shell volume shell_volume	21624 Å³
Envelope diameter envelope_diameter	80.4 Å
Shell Rg shell_rg	27.16 Å
Envelope Rg envelope_rg	21.12 Å
Shape Rg shape_rg	21.16 Å
Total Rg total_rg	21.98 Å
Total atoms total_atoms	2407
Residues n_residues	315
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	74.3 Å
Rg (real space) rg_real	21.88 Å
Rg uncertainty (real space) rg_real_error	0.57 Å
I(0) (real space) i0_real	1.9990e+07
I(0) uncertainty (real space) i0_real_error	2.5940e+05
Rg (reciprocal space) rg_reciprocal	21.90 Å
I(0) (reciprocal space) i0_reciprocal	19990000.0000
Solution quality estimate total_estimate	0.7943
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	28.9 Å
Skewness Skewness skewness	0.189
Kurtosis Kurtosis kurtosis	-0.378
Angular range angular_range	— – 0.3600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6525000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.780; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.000

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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	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 Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	2488

MHHHHHHANVTSIRTEPTYTLYATFDNIGGLKARSPVSIGGVVVGRVADITLDPKTYLPRVTLEIEQRYNHIPDTSSLSIRTSGLLGEQYLALNVGFEDPELGTAILKDGDTIQDTKSAMVLEDLIGQFLYGSKGDDNKNSGDAPAAAPGNNETTEPVGTTK

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 BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	CARBON DIOXIDE
Molecular weight formula_weight	44.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	81

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8. Citations (1)

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Unit-cell length a length_a	60.280 Å
Unit-cell length b length_b	107.290 Å
Unit-cell length c length_c	117.920 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	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	79.360 Å
R factor r_factor	0.2275
R_work r_work	0.2251
R_free r_free	0.2725

fit	/app/data/saxs_computation/hp/8hpz/8hpz.fit
pddf	/app/data/pr_computation/hp/8hpz/8hpz.pr.out
profile	/app/data/saxs_computation/hp/8hpz/8hpz.dat

Crystal structure of the MlaD domain of the MlaD protein from Escherichia coli (Form I)

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