SAXSdb — 8zke

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

Muropeptide transporter

Yokenella regensburgei

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 1–494	Not recorded	2YP (2R)-2-[[(1R,2S,3R,4R,5R)-4-acetamido-2-[(2S,3R,4R,5S,6R)-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl]oxy-6,8-dioxabicyclo[3.2.1]octan-3-yl]oxy]propanoic acid × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.72 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 8ZKE	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8ZBB Cryo-EM structure of outward state Anhydromuropeptide permease (AmpG) G50W/L269W Deposited 2024-04-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 12–198（187 aa） Chain A 203–490（288 aa）	Mutation：G50W/L269W Mutation：G50W/L269W	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.11 Å
9J9Z Cryo-EM structure of Outward state Anhydromuropeptide permease (AmpG) complex with GlcNAc-1,6-anhMurNAc Deposited 2024-08-23	Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 5–198（194 aa） Chain A 203–490（288 aa）	Mutation：G50W/L269W Mutation：G50W/L269W	2YP (2R)-2-[[(1R,2S,3R,4R,5R)-4-acetamido-2-[(2S,3R,4R,5S,6R)-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl]oxy-6,8-dioxabicyclo[3.2.1]octan-3-yl]oxy]propanoic acid × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.97 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0AB38FS76_9ENTR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–494； UniProt 1–494

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	8zke
Deposition date deposition_date	2024-05-16
Structure title title	Cryo-EM structure of inward-facing Anhydromuropeptide permease (AmpG) in complex with GlcNAc-1,6-anhMurNAc
Keywords keywords	AmpG, MFS, Anhydromuropeptide permease, MEMBRANE PROTEIN; MEMBRANE 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	22.03 Å
Radius of gyration Rg (electron density) rg_electron	21.18 Å
Forward intensity I(0) i0	24909000.00
Molecular weight molecular_weight	42365.0 kDa
Excluded volume excluded_volume	54924 Å³
Envelope volume envelope_volume	66195 Å³
Hydration-shell volume shell_volume	25544 Å³
Envelope diameter envelope_diameter	70.8 Å
Shell Rg shell_rg	28.42 Å
Envelope Rg envelope_rg	21.34 Å
Shape Rg shape_rg	21.19 Å
Total Rg total_rg	22.17 Å
Total atoms total_atoms	2987
Residues n_residues	386
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	68.7 Å
Rg (real space) rg_real	21.90 Å
Rg uncertainty (real space) rg_real_error	0.34 Å
I(0) (real space) i0_real	2.4910e+07
I(0) uncertainty (real space) i0_real_error	3.1880e+05
Rg (reciprocal space) rg_reciprocal	21.93 Å
I(0) (reciprocal space) i0_reciprocal	24910000.0000
Solution quality estimate total_estimate	0.9009
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	67.6 Å
Skewness Skewness skewness	0.188
Kurtosis Kurtosis kurtosis	-0.447
Angular range angular_range	— – 0.3600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6108000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.915; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.966

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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	Muropeptide transporter
Molecular weight formula_weight	54069.1 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	2987

MANHYLRIFQQPKSAILLILGFASGLPLALTSGTLQAWMTVENIDLKTIGFFSLVGQAYVFKFLWSPVMDRYTPPFLGRRRGWLVTTQILLLIAIAAMGFLEPGTQLRWMAALAVVIAFCSASQDIVFDAWKTDVLPAEERGTGAAISVLGYRLGMLVSGGLALWMADKWLGWQGMYWLMAALLVPCIIATLLAPEPSDVVPVPRTLEQAVVAPLRDFFGRNNAWLILLLIVLYKLGDAFAMSLTTTFLIRGVGFDAGEVGMVNKTLGLIATIIGALYGGVLMQRLSLFRALLIFGILQGVSNAGYWLLSITDKHLMSMAVAVFFENLCGGMGTAAFVALLMTLCNKSFSATQFALLSALSAVGRVYVGPIAGWFVEAHGWPTFYLFSVFAAVPGILLLLICRKTLEYTQQTESFMMRRHFSGAYQFALYLLLLGCLLLALWLIMLALNAIDYTSFSFLAGLLEVAALIAIAGVLLGAILDYLALRRTEEHKLA

来源 Source

来源生物 organism	Yokenella regensburgei
NCBI Class编号 ncbi_taxonomy_id	158877
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	;(2R)-2-[[(1R,2S,3R,4R,5R)-4-acetamido-2-[(2S,3R,4R,5S,6R)-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl]oxy-6,8-dioxabicyclo[3.2.1]octan-3-yl]oxy]propanoic acid ;
Molecular weight formula_weight	478.4 kDa
Source method src_method	syn
Copy count entity_count	1

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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	3.72 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	133506

fit	/app/data/saxs_computation/zk/8zke/8zke.fit
pddf	/app/data/pr_computation/zk/8zke/8zke.pr.out
profile	/app/data/saxs_computation/zk/8zke/8zke.dat

Cryo-EM structure of inward-facing Anhydromuropeptide permease (AmpG) in complex with GlcNAc-1,6-anhMurNAc

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

Muropeptide transporter

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

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 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)