SAXSdb — 7vr6

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

Intermembrane phospholipid transport system binding protein MlaC

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 22–211	Not recorded	PEF DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.7 M sodium citrate tribasic dihydrate, 0.1 M Bis-Tris propane pH 7.0	Resolution 2.50 Å R-free 0.217

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 7VR6	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5UWA Structure of E. coli phospholipid binding protein MlaC Deposited 2017-02-20	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–211（190 aa）	Not recorded	8ND (2S)-3-(2-aminoethoxy)propane-1,2-diyl dihexadecanoate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.1 M citric acid pH 3.5 and 1.6 M ammonium sulfate	Resolution 1.50 Å R-free 0.168
5UWA Structure of E. coli phospholipid binding protein MlaC Deposited 2017-02-20	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 22–211（190 aa）	Not recorded	8ND (2S)-3-(2-aminoethoxy)propane-1,2-diyl dihexadecanoate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.1 M citric acid pH 3.5 and 1.6 M ammonium sulfate	Resolution 1.50 Å R-free 0.168
6GKI Structure of E coli MlaC in Variously Loaded States Deposited 2018-05-21	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–211（190 aa）	Not recorded	BR BROMIDE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；289 K；seed grown in (0.1M Na Cacodylate pH 6.5, 2M ammonium sulphate, 0.2M NaCl) seed transferred to drop of (0.09M NaF/Br/I, 0.1M Tris/bicine pH 8.5, 20% glycerol, 10% PEG 4000)	Resolution 2.23 Å R-free 0.236
6GKI Structure of E coli MlaC in Variously Loaded States Deposited 2018-05-21	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 22–211（190 aa）	Not recorded	BR BROMIDE ION × 4 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；289 K；seed grown in (0.1M Na Cacodylate pH 6.5, 2M ammonium sulphate, 0.2M NaCl) seed transferred to drop of (0.09M NaF/Br/I, 0.1M Tris/bicine pH 8.5, 20% glycerol, 10% PEG 4000)	Resolution 2.23 Å R-free 0.236
8I8X Cryo-EM Structure of OmpC3-MlaA-MlaC Complex in MSP2N2 Nanodiscs Deposited 2023-02-05	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 × 5 PDB declaration: pentameric	Chain F 21–211（191 aa）	Mutation：V171C	KDL (2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-[(2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-carboxy-2-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-5-[[(3~{R})-3-dodecanoyloxytetradecanoyl]amino]-6-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-3-oxidanyl-5-[[(3~{R})-3-oxidanyltetradecanoyl]amino]-4-[(3~{R})-3-oxidanyltetradecanoyl]oxy-6-phosphonooxy-oxan-2-yl]methoxy]-3-phosphonooxy-4-[(3~{R})-3-tetradecanoyloxytetradecanoyl]oxy-oxan-2-yl]methoxy]-5-oxidanyl-oxan-4-yl]oxy-4,5-bis(oxidanyl)oxane-2-carboxylic acid × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8；Tris-buffered saline (TBS) buffer (20 mM Tris HCl pH 8.0, 150 mM NaCl) cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.25 Å
8OJ4 Structure of the MlaCD complex (1:6 stoichiometry) Deposited 2023-03-23	Different construct 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 H 1–211（211 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 G 1–211（211 aa） Chain H 1–211（211 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

5 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MLAC_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 8–197； UniProt 22–211

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	7vr6
Deposition date deposition_date	2021-10-21
Structure title title	Crystal structure of MlaC from Escherichia coli in quasi-open state
Keywords keywords	ABC transporter, Periplasmic protein, Membrane lipid asymmetry, Segmented domain movement, Mla transport system, 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	18.36 Å
Radius of gyration Rg (electron density) rg_electron	16.95 Å
Forward intensity I(0) i0	8320900.00
Molecular weight molecular_weight	21902.0 kDa
Excluded volume excluded_volume	27759 Å³
Envelope volume envelope_volume	31681 Å³
Hydration-shell volume shell_volume	15882 Å³
Envelope diameter envelope_diameter	58.4 Å
Shell Rg shell_rg	22.80 Å
Envelope Rg envelope_rg	17.28 Å
Shape Rg shape_rg	16.95 Å
Total Rg total_rg	17.96 Å
Total atoms total_atoms	1544
Residues n_residues	185
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	57.8 Å
Rg (real space) rg_real	18.26 Å
Rg uncertainty (real space) rg_real_error	0.31 Å
I(0) (real space) i0_real	8.3210e+06
I(0) uncertainty (real space) i0_real_error	9.8740e+04
Rg (reciprocal space) rg_reciprocal	18.28 Å
I(0) (reciprocal space) i0_reciprocal	8321000.0000
Solution quality estimate total_estimate	0.9002
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.4 Å
Skewness Skewness skewness	0.139
Kurtosis Kurtosis kurtosis	-0.458
Angular range angular_range	— – 0.4350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1080000.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.913; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.965

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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 MlaC
Molecular weight formula_weight	22717.8 kDa
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	1616

MHHHHHHADQTNPYKLMDEAAQKTFDRLKNEQPQIRANPDYLRTIVDQELLPYVQVKYAGALVLGQYYKSATPAQREAYFAAFREYLKQAYGQALAMYHGQTYQIAPEQPLGDKTIVPIRVTIIDPNGRPPVRLDFQWRKNSQTGNWQAYDMIAEGVSMITTKQNEWGTLLRTKGIDGLTAQLKSISQQKITLEEKK

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	DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE
Molecular weight formula_weight	692.0 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	58

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8. Citations (1)

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Unit-cell length a length_a	114.940 Å
Unit-cell length b length_b	114.940 Å
Unit-cell length c length_c	46.100 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	9

Space group space_group	H 3
Space-group number int_tables_number	146
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	57.470 Å
R factor r_factor	0.1714
R_work r_work	0.1691
R_free r_free	0.2170

fit	/app/data/saxs_computation/vr/7vr6/7vr6.fit
pddf	/app/data/pr_computation/vr/7vr6/7vr6.pr.out
profile	/app/data/saxs_computation/vr/7vr6/7vr6.dat

Crystal structure of MlaC from Escherichia coli in quasi-open state

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

Intermembrane phospholipid transport system binding protein MlaC

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