SAXSdb — 6nm5

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

Type IV conjugative transfer system pilin TraA

OrganismNot specified

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 × 76 PDB declaration: 76-meric（76） Consistent with protein copy count	Chain 1A； UniProt 30–94 Chain 1B； UniProt 30–94 Chain 1C； UniProt 30–94 Chain 1D； UniProt 30–94 Chain 1E； UniProt 30–94 Chain 1F； UniProt 30–94 Chain 1G； UniProt 30–94 Chain 1H； UniProt 30–94 Chain 1I； UniProt 30–94 Chain 1J； UniProt 30–94 Chain 1K； UniProt 30–94 Chain 1L； UniProt 30–94 Chain 1M； UniProt 30–94 Chain 1N； UniProt 30–94 Chain 1O； UniProt 30–94 Chain 2A； UniProt 30–94 Chain 2B； UniProt 30–94 Chain 2C； UniProt 30–94 Chain 2D； UniProt 30–94 Chain 2E； UniProt 30–94 Chain 2F； UniProt 30–94 Chain 2G； UniProt 30–94 Chain 2H； UniProt 30–94 Chain 2I； UniProt 30–94 Chain 2J； UniProt 30–94 Chain 2K； UniProt 30–94 Chain 2L； UniProt 30–94 Chain 2M； UniProt 30–94 Chain 2N； UniProt 30–94 Chain 2O； UniProt 30–94 Chain 3A； UniProt 30–94 Chain 3B； UniProt 30–94 Chain 3C； UniProt 30–94 Chain 3D； UniProt 30–94 Chain 3E； UniProt 30–94 Chain 3F； UniProt 30–94 Chain 3G； UniProt 30–94 Chain 3H； UniProt 30–94 Chain 3I； UniProt 30–94 Chain 3J； UniProt 30–94 Chain 3K； UniProt 30–94 Chain 3L； UniProt 30–94 Chain 3M； UniProt 30–94 Chain 3N； UniProt 30–94 Chain 3O； UniProt 30–94 Chain 4A； UniProt 30–94 Chain 4B； UniProt 30–94 Chain 4C； UniProt 30–94 Chain 4D； UniProt 30–94 Chain 4E； UniProt 30–94 Chain 4F； UniProt 30–94 Chain 4G； UniProt 30–94 Chain 4H； UniProt 30–94 Chain 4I； UniProt 30–94 Chain 4J； UniProt 30–94 Chain 4K； UniProt 30–94 Chain 4L； UniProt 30–94 Chain 4M； UniProt 30–94 Chain 4N； UniProt 30–94 Chain 4O； UniProt 30–94 Chain 5A； UniProt 30–94 Chain 5B； UniProt 30–94 Chain 5C； UniProt 30–94 Chain 5D； UniProt 30–94 Chain 5E； UniProt 30–94 Chain 5F； UniProt 30–94 Chain 5G； UniProt 30–94 Chain 5H； UniProt 30–94 Chain 5I； UniProt 30–94 Chain 5J； UniProt 30–94 Chain 5K； UniProt 30–94 Chain 5L； UniProt 30–94 Chain 5M； UniProt 30–94 Chain 5N； UniProt 30–94 Chain 5O； UniProt 30–94	Not recorded	Maturation protein × 1 （P03610） KSV (2R)-2,3-dihydroxypropyl ethyl hydrogen (S)-phosphate × 70	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 6.20 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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	A0A1Y2ZDR2_ECOLX
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain 1A； PDBConstruct 1–65； UniProt 30–94 Author chain 1B； PDBConstruct 1–65； UniProt 30–94 Author chain 1C； PDBConstruct 1–65； UniProt 30–94 Author chain 1D； PDBConstruct 1–65； UniProt 30–94 Author chain 1E； PDBConstruct 1–65； UniProt 30–94 Author chain 1F； PDBConstruct 1–65； UniProt 30–94 Author chain 1G； PDBConstruct 1–65； UniProt 30–94 Author chain 1H； PDBConstruct 1–65； UniProt 30–94 Author chain 1I； PDBConstruct 1–65； UniProt 30–94 Author chain 1J； PDBConstruct 1–65； UniProt 30–94 Author chain 1K； PDBConstruct 1–65； UniProt 30–94 Author chain 1L； PDBConstruct 1–65； UniProt 30–94 Author chain 1M； PDBConstruct 1–65； UniProt 30–94 Author chain 1N； PDBConstruct 1–65； UniProt 30–94 Author chain 1O； PDBConstruct 1–65； UniProt 30–94 Author chain 2A； PDBConstruct 1–65； UniProt 30–94 Author chain 2B； PDBConstruct 1–65； UniProt 30–94 Author chain 2C； PDBConstruct 1–65； UniProt 30–94 Author chain 2D； PDBConstruct 1–65； UniProt 30–94 Author chain 2E； PDBConstruct 1–65； UniProt 30–94 Author chain 2F； PDBConstruct 1–65； UniProt 30–94 Author chain 2G； PDBConstruct 1–65； UniProt 30–94 Author chain 2H； PDBConstruct 1–65； UniProt 30–94 Author chain 2I； PDBConstruct 1–65； UniProt 30–94 Author chain 2J； PDBConstruct 1–65； UniProt 30–94 Author chain 2K； PDBConstruct 1–65； UniProt 30–94 Author chain 2L； PDBConstruct 1–65； UniProt 30–94 Author chain 2M； PDBConstruct 1–65； UniProt 30–94 Author chain 2N； PDBConstruct 1–65； UniProt 30–94 Author chain 2O； PDBConstruct 1–65； UniProt 30–94 Author chain 3A； PDBConstruct 1–65； UniProt 30–94 Author chain 3B； PDBConstruct 1–65； UniProt 30–94 Author chain 3C； PDBConstruct 1–65； UniProt 30–94 Author chain 3D； PDBConstruct 1–65； UniProt 30–94 Author chain 3E； PDBConstruct 1–65； UniProt 30–94 Author chain 3F； PDBConstruct 1–65； UniProt 30–94 Author chain 3G； PDBConstruct 1–65； UniProt 30–94 Author chain 3H； PDBConstruct 1–65； UniProt 30–94 Author chain 3I； PDBConstruct 1–65； UniProt 30–94 Author chain 3J； PDBConstruct 1–65； UniProt 30–94 Author chain 3K； PDBConstruct 1–65； UniProt 30–94 Author chain 3L； PDBConstruct 1–65； UniProt 30–94 Author chain 3M； PDBConstruct 1–65； UniProt 30–94 Author chain 3N； PDBConstruct 1–65； UniProt 30–94 Author chain 3O； PDBConstruct 1–65； UniProt 30–94 Author chain 4A； PDBConstruct 1–65； UniProt 30–94 Author chain 4B； PDBConstruct 1–65； UniProt 30–94 Author chain 4C； PDBConstruct 1–65； UniProt 30–94 Author chain 4D； PDBConstruct 1–65； UniProt 30–94 Author chain 4E； PDBConstruct 1–65； UniProt 30–94 Author chain 4F； PDBConstruct 1–65； UniProt 30–94 Author chain 4G； PDBConstruct 1–65； UniProt 30–94 Author chain 4H； PDBConstruct 1–65； UniProt 30–94 Author chain 4I； PDBConstruct 1–65； UniProt 30–94 Author chain 4J； PDBConstruct 1–65； UniProt 30–94 Author chain 4K； PDBConstruct 1–65； UniProt 30–94 Author chain 4L； PDBConstruct 1–65； UniProt 30–94 Author chain 4M； PDBConstruct 1–65； UniProt 30–94 Author chain 4N； PDBConstruct 1–65； UniProt 30–94 Author chain 4O； PDBConstruct 1–65； UniProt 30–94 Author chain 5A； PDBConstruct 1–65； UniProt 30–94 Author chain 5B； PDBConstruct 1–65； UniProt 30–94 Author chain 5C； PDBConstruct 1–65； UniProt 30–94 Author chain 5D； PDBConstruct 1–65； UniProt 30–94 Author chain 5E； PDBConstruct 1–65； UniProt 30–94 Author chain 5F； PDBConstruct 1–65； UniProt 30–94 Author chain 5G； PDBConstruct 1–65； UniProt 30–94 Author chain 5H； PDBConstruct 1–65； UniProt 30–94 Author chain 5I； PDBConstruct 1–65； UniProt 30–94 Author chain 5J； PDBConstruct 1–65； UniProt 30–94 Author chain 5K； PDBConstruct 1–65； UniProt 30–94 Author chain 5L； PDBConstruct 1–65； UniProt 30–94 Author chain 5M； PDBConstruct 1–65； UniProt 30–94 Author chain 5N； PDBConstruct 1–65； UniProt 30–94 Author chain 5O； PDBConstruct 1–65； UniProt 30–94

Maturation protein

OrganismNot specified

UniProt P03610

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 × 76 PDB declaration: 76-meric（76） Consistent with protein copy count	Chain M； UniProt 1–393	Not recorded	Type IV conjugative transfer system pilin TraA × 75 （A0A1Y2ZDR2） KSV (2R)-2,3-dihydroxypropyl ethyl hydrogen (S)-phosphate × 70	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 6.20 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 6NM5	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5TC1 In situ structures of the genome and genome-delivery apparatus in ssRNA bacteriophage MS2 Deposited 2016-09-13	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 9 PDB declaration: decameric	Chain M 1–393（393 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；pH7.4 PBS cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å

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

View Construct and Data Evidence

UniProt name	MAT_BPMS2
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain M； PDBConstruct 1–393； UniProt 1–393

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	6nm5
Deposition date deposition_date	2019-01-10
Structure title title	F-pilus/MS2 Maturation protein complex
Keywords keywords	MS2 maturation protein, F-pilus, adsorption complex, PROTEIN BINDING; PROTEIN BINDING
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	65.57 Å
Radius of gyration Rg (electron density) rg_electron	65.90 Å
Forward intensity I(0) i0	3800760000.00
Molecular weight molecular_weight	568830.0 kDa
Excluded volume excluded_volume	733170 Å³
Envelope volume envelope_volume	1148900 Å³
Hydration-shell volume shell_volume	148680 Å³
Envelope diameter envelope_diameter	248.3 Å
Shell Rg shell_rg	63.95 Å
Envelope Rg envelope_rg	65.65 Å
Shape Rg shape_rg	65.91 Å
Total Rg total_rg	65.83 Å
Total atoms total_atoms	39163
Residues n_residues	5207
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	254.7 Å
Rg (real space) rg_real	69.82 Å
Rg uncertainty (real space) rg_real_error	1.78 Å
I(0) (real space) i0_real	3.8400e+09
I(0) uncertainty (real space) i0_real_error	8.2480e+07
Rg (reciprocal space) rg_reciprocal	65.05 Å
I(0) (reciprocal space) i0_reciprocal	3793000000.0000
Solution quality estimate total_estimate	0.8144
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	63.7 Å
Skewness Skewness skewness	0.720
Kurtosis Kurtosis kurtosis	0.148
Angular range angular_range	— – 0.1200 Å⁻¹
Current regularization parameter α current_alpha	0.8319
Highest regularization parameter α highest_alpha	1554000000.0000
Real-space data points n_real_points	25
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.470; Stabil: 0.871; Sysdev: 1.000; Positv: 1.000; Valcen: 0.964; Smooth: 0.741

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Type IV conjugative transfer system pilin TraA
Molecular weight formula_weight	6831.2 kDa
Source method src_method	nat
Copy count entity_count	75

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	;1A,1B,1C,1D,1E,1F,1G,1H,1I,1J,1K,1L,1M,1N,1O,2A,2B,2C,2D,2E,2F,2G,2H,2I,2J,2K,2L,2M,2N,2O,3A,3B,3C,3D,3E,3F,3G,3H,3I,3J,3K,3L,3M,3N,3O,4A,4B,4C,4D,4E,4F,4G,4H,4I,4J,4K,4L,4M,4N,4O,5A,5B,5C,5D,5E,5F,5G,5H,5I,5J,5K,5L,5M,5N,5O ;
Atom count atom_count	39224

QDLMASGNTTVKATFGKDSSVVKWVVLAEVLVGAVMYMMTKNVKFLAGFAIISVFIAVGMAVVGL

Entity 2 Entity 2 polymer

Description description	Maturation protein
Molecular weight formula_weight	44030.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M

MRAFSTLDRENETFVPSVRVYADGETEDNSFSLKYRSNWTPGRFNSTGAKTKQWHYPSPYSRGALSVTSIDQGAYKRSGSSWGRPYEEKAGFGFSLDARSCYSLFPVSQNLTYIEVPQNVANRASTEVLQKVTQGNFNLGVALAEARSTASQLATQTIALVKAYTAARRGNWRQALRYLALNEDRKFRSKHVAGRWLELQFGWLPLMSDIQGAYEMLTKVHLQEFLPMRAVRQVGTNIKLDGRLSYPAANFQTTCNISRRIVIWFYINDARLAWLSSLGILNPLGIVWEKVPFSFVVDWLLPVGNMLEGLTAPVGCSYMSGTVTDVITGESIISVDAPYGWTVERQGTAKAQISAMHRGVQSVWPTTGAYVKSPFSMVHTLDALALIRQRLSR

Entity 3 Entity 3 non-polymer

Description description	(2R)-2,3-dihydroxypropyl ethyl hydrogen (S)-phosphate
Molecular weight formula_weight	200.1 kDa
Source method src_method	syn
Copy count entity_count	70

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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	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	triclinic

Resolution resolution	6.20 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	168989

fit	/app/data/saxs_computation/nm/6nm5/6nm5.fit
pddf	/app/data/pr_computation/nm/6nm5/6nm5.pr.out
profile	/app/data/saxs_computation/nm/6nm5/6nm5.dat

F-pilus/MS2 Maturation protein complex

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

Type IV conjugative transfer system pilin TraA

State in the Current Structure

Other States of the Same Protein in the Database

Maturation 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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)