SAXSdb — 9nu4

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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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 3–500	Mutation：K5F, S12I, M13A	Lysis protein × 1 （K7QK87）	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.60 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 9NU4	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 method 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
7WAG Crystal structure of MurJ squeezed form Deposited 2021-12-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–511（510 aa）	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
9NU5 Structure of MurJ in complex with single gene lysis protein from phage PP7 Deposited 2025-03-19	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	Parsed fields agree	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 construct Different mutation/modification 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 107–604； UniProt 3–500

Lysis protein

Enterobacteria phage M

UniProt K7QK87

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 2–37	Not recorded	Lipid II flippase MurJ × 1 （P0AF16）	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.60 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 9NU4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9UKV JM Complex - E. coli MurJ, Levivirus M lysis protein LysM (SglM) Deposited 2025-04-18	Different construct Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–37（37 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

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	K7QK87_BPM
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 31–66； UniProt 2–37

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	9nu4
Deposition date deposition_date	2025-03-19
Structure title title	Structure of MurJ in complex with single gene lysis protein from phage M
Keywords keywords	lipid II flippase, phage single gene lysis proteins, peptidoglycan biosynthesis, TRANSPORT PROTEIN; TRANSPORT PROTEIN
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	27.07 Å
Radius of gyration Rg (electron density) rg_electron	25.92 Å
Forward intensity I(0) i0	63161800.00
Molecular weight molecular_weight	68406.0 kDa
Excluded volume excluded_volume	88521 Å³
Envelope volume envelope_volume	106360 Å³
Hydration-shell volume shell_volume	33876 Å³
Envelope diameter envelope_diameter	86.5 Å
Shell Rg shell_rg	33.74 Å
Envelope Rg envelope_rg	25.79 Å
Shape Rg shape_rg	25.92 Å
Total Rg total_rg	26.85 Å
Total atoms total_atoms	4824
Residues n_residues	631
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	84.0 Å
Rg (real space) rg_real	26.96 Å
Rg uncertainty (real space) rg_real_error	0.38 Å
I(0) (real space) i0_real	6.3160e+07
I(0) uncertainty (real space) i0_real_error	7.9260e+05
Rg (reciprocal space) rg_reciprocal	27.00 Å
I(0) (reciprocal space) i0_reciprocal	63160000.0000
Solution quality estimate total_estimate	0.9071
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	34.1 Å
Skewness Skewness skewness	0.223
Kurtosis Kurtosis kurtosis	-0.444
Angular range angular_range	— – 0.2950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8221000.0000
Real-space data points n_real_points	60
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.940; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.968

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Lipid II flippase MurJ
Molecular weight formula_weight	66668.7 kDa
Mutation mutation	K5F, S12I, M13A
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	4824

MADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLLFSLAAVSIATMFSRVLGFARDAIVARIFGAGMATDAFFVAFKLPNLLRRIFAEGAFSQAFVPILAEYKSKQGEDATRVFVSYVSGLLTLALAVVTVAGMLAAPWVIMVTAPGFADTADKFALTSQLLKITFPYILLISLASLVGAILNTWNRFSIPAFAPTLLNISMIGFALFAAPYFNPPVLALAWAVTVGGVLQLVYQLPHLKKIGMLVLPRINFHDAGAMRVVKQMGPAILGVSVSQISLIINTIFASFLASGSVSWMYYADRLMEFPSGVLGVALGTILLPSLSKSFASGNHDEYNRLMDWGLRLCFLLALPSAVALGILSGPLTVSLFQYGKFTAFDALMTQRALIAYSVGLIGLIVVKVLAPGFYSRQDIKTPVKIAIVTLILTQLMNLAFIGPLKHAGLSLSIGLAACLNASLLYWQLRKQKIFTPQPGWMAFLLRLVVAVLVMSGVLLGMLHIMPEWSLGTMPWRLLRLMAVVLAGIAAYFAALAVLGSAWSHPQFEK

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 polymer

Description description	Lysis protein
Molecular weight formula_weight	6625.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MGHHHHHHGSGSGSGSGSGSGSGSGSGSGSKYIINLAFCVLLLVAGDSIAYRVSQYLAPLVDTFTK

来源 Source

来源生物 organism	Enterobacteria phage M
NCBI Class编号 ncbi_taxonomy_id	1235640
宿主生物 host_organism	Escherichia coli BL21(DE3)

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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	3.600 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	3.60 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	61237

fit	/app/data/saxs_computation/nu/9nu4/9nu4.fit
pddf	/app/data/pr_computation/nu/9nu4/9nu4.pr.out
profile	/app/data/saxs_computation/nu/9nu4/9nu4.dat

Structure of MurJ in complex with single gene lysis protein from phage M

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

Lysis protein

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)