SAXSdb — 7wag

▼

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

Lipid II flippase MurJ

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 2–511	Mutation：v10R, S11C	OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 13 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions：LIPIDIC CUBIC PHASE；293.15 K；MPD, MgCl2, Tris-HCl, PEG, OLC	Resolution 2.55 Å R-free 0.268

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 7WAG	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6CC4 Structure of MurJ from Escherichia coli Deposited 2018-02-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 4–511（508 aa）	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 6；293 K；100 mM MES, pH 6.0, 100 mM potassium phosphate dibasic, 28% PEG300, 1% 1,2,3-heptanetriol, lipid stock used for reconstitution was 10:1 w/w monoolein:cholesterol	Resolution 3.50 Å R-free 0.301
9NU4 Structure of MurJ in complex with single gene lysis protein from phage M Deposited 2025-03-19	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 × 2 PDB declaration: dimeric	Chain A 3–500（498 aa）	Mutation：K5F, S12I, M13A	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
9NU5 Structure of MurJ in complex with single gene lysis protein from phage PP7 Deposited 2025-03-19	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 × 2 PDB declaration: dimeric	Chain A 3–500（498 aa）	Mutation：K5F, S12I, M13A	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
9NU8 Structure of MurJ in complex with single gene lysis protein from phage Changjiang3 Deposited 2025-03-19	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 × 2 PDB declaration: dimeric	Chain A 3–500（498 aa）	Mutation：K5F, S12I, M13A	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
9UKV JM Complex - E. coli MurJ, Levivirus M lysis protein LysM (SglM) Deposited 2025-04-18	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 × 2 PDB declaration: dimeric	Chain A 2–511（510 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.05 Å

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

View Construct and Data Evidence

UniProt name	MURJ_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–511； UniProt 2–511

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	7wag
Deposition date deposition_date	2021-12-14
Structure title title	Crystal structure of MurJ squeezed form
Keywords keywords	14 transmembrane helices, inner membrane, Lipid II, MOP superfamily, LIPID TRANSPORT; LIPID TRANSPORT
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	24.39 Å
Radius of gyration Rg (electron density) rg_electron	23.46 Å
Forward intensity I(0) i0	42323300.00
Molecular weight molecular_weight	59739.0 kDa
Excluded volume excluded_volume	78903 Å³
Envelope volume envelope_volume	89935 Å³
Hydration-shell volume shell_volume	31004 Å³
Envelope diameter envelope_diameter	79.5 Å
Shell Rg shell_rg	31.36 Å
Envelope Rg envelope_rg	23.45 Å
Shape Rg shape_rg	23.45 Å
Total Rg total_rg	24.52 Å
Total atoms total_atoms	4213
Residues n_residues	522
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

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	76.2 Å
Rg (real space) rg_real	24.23 Å
Rg uncertainty (real space) rg_real_error	0.43 Å
I(0) (real space) i0_real	4.2320e+07
I(0) uncertainty (real space) i0_real_error	5.7020e+05
Rg (reciprocal space) rg_reciprocal	24.27 Å
I(0) (reciprocal space) i0_reciprocal	42320000.0000
Solution quality estimate total_estimate	0.9025
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	31.5 Å
Skewness Skewness skewness	0.124
Kurtosis Kurtosis kurtosis	-0.511
Angular range angular_range	— – 0.3250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5639000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.917; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.981

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Lipid II flippase MurJ
Molecular weight formula_weight	56579.4 kDa
Mutation mutation	v10R, S11C
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	4273

NLLKSLAAGRCSMTMFSRVLGFARDAIVARIFGAGMATDAFFVAFKLPNLLRRIFAEGAFSQAFVPILAEYKSKQGEDATRVFVSYVSGLLTLALAVVTVAGMLAAPWVIMVTAPGFADTADKFALTSQLLKITFPYILLISLASLVGAILNTWNRFSIPAFAPTLLNISMIGFALFAAPYFNPPVLALAWAVTVGGVLQLVYQLPHLKKIGMLVLPRINFHDAGAMRVVKQMGPAILGVSVSQISLIINTIFASFLASGSVSWMYYADRLMEFPSGVLGVALGTILLPSLSKSFASGNHDEYNRLMDWGLRLCFLLALPSAVALGILSGPLTVSLFQYGKFTAFDALMTQRALIAYSVGLIGLIVVKVLAPGFYSRQDIKTPVKIAIVTLILTQLMNLAFIGPLKHAGLSLSIGLAACLNASLLYWQLRKQKIFTPQPGWMAFLLRLVVAVLVMSGVLLGMLHIMPEWSLGTMPWRLLRLMAVVLAGIAAYFAALAVLGFKVKEFARRTVLESSGENLYFQ

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	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
Molecular weight formula_weight	356.5 kDa
Source method src_method	syn
Copy count entity_count	13

Entity 3 Entity 3 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 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	60

▶

8. Citations (1)

▶

Unit-cell length a length_a	74.450 Å
Unit-cell length b length_b	75.060 Å
Unit-cell length c length_c	115.210 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.550 Å
Low-resolution limit resolution_low	45.700 Å
R factor r_factor	0.2195
R_work r_work	0.2145
R_free r_free	0.2680

fit	/app/data/saxs_computation/wa/7wag/7wag.fit
pddf	/app/data/pr_computation/wa/7wag/7wag.pr.out
profile	/app/data/saxs_computation/wa/7wag/7wag.dat

Crystal structure of MurJ squeezed form

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

Lipid II flippase MurJ

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