SAXSdb — 5mfd

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

Capsid decoration protein,pD_(KR)5

Enterobacteria phage lambda

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 21–110	Fragment：UNP residues 21-110	YIIIM''6AII × 1 CA CALCIUM ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；28.0%v/v PEG 400, 0.2M Calcium chloride, 0.1M Na HEPES pH 7.5	Resolution 2.30 Å R-free 0.214
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 21–110	Fragment：UNP residues 21-110	YIIIM''6AII × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；28.0%v/v PEG 400, 0.2M Calcium chloride, 0.1M Na HEPES pH 7.5	Resolution 2.30 Å R-free 0.214
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain F； UniProt 21–110	Fragment：UNP residues 21-110	YIIIM''6AII × 1 CA CALCIUM ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；28.0%v/v PEG 400, 0.2M Calcium chloride, 0.1M Na HEPES pH 7.5	Resolution 2.30 Å R-free 0.214
4	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain H； UniProt 21–110	Fragment：UNP residues 21-110	YIIIM''6AII × 1 CA CALCIUM ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；28.0%v/v PEG 400, 0.2M Calcium chloride, 0.1M Na HEPES pH 7.5	Resolution 2.30 Å R-free 0.214

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 5MFD	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1C5E BACTERIOPHAGE LAMBDA HEAD PROTEIN D Deposited 1999-11-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 16–110（95 aa） Chain B 16–110（95 aa） Chain C 16–110（95 aa）	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；28% PEG 4000, 0.1 M BIS-TRIS PH 6.5, 10 % GLYCEROL	Resolution 1.10 Å R-free 0.133
1TCZ Crystal structure of a truncated version of the phage lamda protein gpD Deposited 2004-05-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 16–110（95 aa） Fragment：N-terminal truncation Chain B 16–110（95 aa） Fragment：N-terminal truncation Chain C 16–110（95 aa） Fragment：N-terminal truncation	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；Tris-HCl, PEG 4000, Mg acetate, glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.85 Å R-free 0.232
1TCZ Crystal structure of a truncated version of the phage lamda protein gpD Deposited 2004-05-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain D 16–110（95 aa） Fragment：N-terminal truncation Chain E 16–110（95 aa） Fragment：N-terminal truncation Chain F 16–110（95 aa） Fragment：N-terminal truncation	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；Tris-HCl, PEG 4000, Mg acetate, glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.85 Å R-free 0.232
1VD0 Capsid stabilizing protein GPD, NMR, 20 Structures Deposited 2004-03-17	Different construct 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 2–110（109 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；298 K；Pressure AMBIENT NMR sample composition 1.3mm 15N labelled GPD, 20mm sodium phosphate \| 90% H2O/10% D2O NMR sample composition 1.3mm GPD, 50mm sodium phosphate \| 100% D2O	Resolution not provided
7VII cryoEM structure of bacteriophage lambda capsid at 5.6 Angstrom Deposited 2021-09-27	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 × 840 PDB declaration: 840-meric	Chain H 1–110（110 aa） Chain I 1–110（110 aa） Chain J 1–110（110 aa） Chain K 1–110（110 aa） Chain L 1–110（110 aa） Chain M 1–110（110 aa） Chain N 1–110（110 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 5.60 Å
7VII cryoEM structure of bacteriophage lambda capsid at 5.6 Angstrom Deposited 2021-09-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain H 1–110（110 aa） Chain I 1–110（110 aa） Chain J 1–110（110 aa） Chain K 1–110（110 aa） Chain L 1–110（110 aa） Chain M 1–110（110 aa） Chain N 1–110（110 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 5.60 Å
7VII cryoEM structure of bacteriophage lambda capsid at 5.6 Angstrom Deposited 2021-09-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 70 PDB declaration: 70-meric	Chain H 1–110（110 aa） Chain I 1–110（110 aa） Chain J 1–110（110 aa） Chain K 1–110（110 aa） Chain L 1–110（110 aa） Chain M 1–110（110 aa） Chain N 1–110（110 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 5.60 Å
7VII cryoEM structure of bacteriophage lambda capsid at 5.6 Angstrom Deposited 2021-09-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 84 PDB declaration: 84-meric	Chain H 1–110（110 aa） Chain I 1–110（110 aa） Chain J 1–110（110 aa） Chain K 1–110（110 aa） Chain L 1–110（110 aa） Chain M 1–110（110 aa） Chain N 1–110（110 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 5.60 Å
7VII cryoEM structure of bacteriophage lambda capsid at 5.6 Angstrom Deposited 2021-09-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain H 1–110（110 aa） Chain I 1–110（110 aa） Chain J 1–110（110 aa） Chain K 1–110（110 aa） Chain L 1–110（110 aa） Chain M 1–110（110 aa） Chain N 1–110（110 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 5.60 Å
7VIK Asymmetric unit of cryoEM structure of bacteriophage lambda capsid at 3.76 Angstrom Deposited 2021-09-27	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 × 14 PDB declaration: tetradecameric	Chain H 1–110（110 aa） Chain I 1–110（110 aa） Chain J 1–110（110 aa） Chain K 1–110（110 aa） Chain L 1–110（110 aa） Chain M 1–110（110 aa） Chain N 1–110（110 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.76 Å
8XQB Mature virion portal vertex of bacteriophage lambda Deposited 2024-01-05	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 × 71 PDB declaration: 71-meric	Chain H0 1–110（110 aa） Chain H1 1–110（110 aa） Chain H2 1–110（110 aa） Chain H3 1–110（110 aa） Chain H4 1–110（110 aa） Chain I0 1–110（110 aa） Chain I1 1–110（110 aa） Chain I2 1–110（110 aa） Chain I3 1–110（110 aa） Chain I4 1–110（110 aa） Chain J0 1–110（110 aa） Chain J1 1–110（110 aa） Chain J2 1–110（110 aa） Chain J3 1–110（110 aa） Chain J4 1–110（110 aa） Chain N0 1–110（110 aa） Chain N1 1–110（110 aa） Chain N2 1–110（110 aa） Chain N3 1–110（110 aa） Chain N4 1–110（110 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 4.07 Å

6 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DECO_LAMBD
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 3–92； UniProt 21–110 Author chain D； PDBConstruct 3–92； UniProt 21–110 Author chain F； PDBConstruct 3–92； UniProt 21–110 Author chain H； PDBConstruct 3–92； UniProt 21–110

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	5mfd
Deposition date deposition_date	2016-11-18
Structure title title	Designed armadillo repeat protein YIIIM''6AII in complex with pD_(KR)5
Keywords keywords	Designed armadillo repeat protein, peptide binding, de novo protein; DE NOVO 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	73.88 Å
Radius of gyration Rg (electron density) rg_electron	75.51 Å
Forward intensity I(0) i0	1433820000.00
Molecular weight molecular_weight	317210.0 kDa
Excluded volume excluded_volume	397330 Å³
Envelope volume envelope_volume	590030 Å³
Hydration-shell volume shell_volume	77150 Å³
Envelope diameter envelope_diameter	281.5 Å
Shell Rg shell_rg	54.92 Å
Envelope Rg envelope_rg	74.93 Å
Shape Rg shape_rg	75.52 Å
Total Rg total_rg	75.03 Å
Total atoms total_atoms	22255
Residues n_residues	3005
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	230.9 Å
Rg (real space) rg_real	73.08 Å
Rg uncertainty (real space) rg_real_error	1.95 Å
I(0) (real space) i0_real	1.4220e+09
I(0) uncertainty (real space) i0_real_error	2.9390e+07
Rg (reciprocal space) rg_reciprocal	70.01 Å
I(0) (reciprocal space) i0_reciprocal	1420000000.0000
Solution quality estimate total_estimate	0.7787
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	44.0 Å
Skewness Skewness skewness	0.585
Kurtosis Kurtosis kurtosis	-0.453
Angular range angular_range	— – 0.1050 Å⁻¹
Current regularization parameter α current_alpha	0.0352
Highest regularization parameter α highest_alpha	29780000.0000
Real-space data points n_real_points	22
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.713; Stabil: 0.990; Sysdev: 1.000; Positv: 1.000; Valcen: 0.787; Smooth: 0.191

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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	YIIIM''6AII
Molecular weight formula_weight	34353.3 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G,I,J,K,L
Atom count atom_count	22833

GPGSELPQMVQQLNSPDQQELQSALRKLSQIASGGNEQIQAVIDAGALPALVQLLSSPNEQILQEALWTLGNIASGGNEQIQAVIDAGALPALVQLLSSPNEQILQEALWTLGNIASGGNEQIQAVIDAGALPALVQLLSSPNEQILQEALWTLGNIASGGNEQIQAVIDAGALPALVQLLSSPNEQILQEALWTLGNIASGGNEQIQAVIDAGALPALVQLLSSPNEQILQEALWTLGNIASGGNEQIQAVIDAGALPALVQLLSSPNEQILQEALWTLGNIASGGNEQKQAVKEAGALEKLEQLQSHENEKIQKEAQEALEKLQSH

来源 Source

来源生物 organism	synthetic construct
NCBI Class编号 ncbi_taxonomy_id	32630
宿主生物 host_organism	Escherichia coli K-12

Entity 2 Entity 2 polymer

Description description	Capsid decoration protein,pD_(KR)5
Molecular weight formula_weight	11479.0 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F,H

GPTATAPGGLSAKAPAMTPLMLDTSSRKLVAWDGTTDGAAVGILAVAADQTSTTLTFYKSGTFRYEDVLWPEAASDETKKRTAFAGTAISIVGSGSPKRKRKRKRKREG

来源 Source

来源生物 organism	Enterobacteria phage lambda
NCBI Class编号 ncbi_taxonomy_id	10710
宿主生物 host_organism	Escherichia coli K-12

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	49

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	485

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7. Fold Classification (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

Domain ID domain_id	5mfdB00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	300 — Virus Head Decoration Protein; Chain: A,
Homologous superfamily homologous superfamily	10 — Head decoration protein D

Domain ID domain_id	5mfdD00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	300 — Virus Head Decoration Protein; Chain: A,
Homologous superfamily homologous superfamily	10 — Head decoration protein D

Domain ID domain_id	5mfdF00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	300 — Virus Head Decoration Protein; Chain: A,
Homologous superfamily homologous superfamily	10 — Head decoration protein D

Domain ID domain_id	5mfdH00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	300 — Virus Head Decoration Protein; Chain: A,
Homologous superfamily homologous superfamily	10 — Head decoration protein D

Domain ID domain_id	5mfdI00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	10 — Leucine-rich Repeat Variant
Homologous superfamily homologous superfamily	10 — Leucine-rich Repeat Variant

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8. Citations (1)

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Unit-cell length a length_a	194.660 Å
Unit-cell length b length_b	194.660 Å
Unit-cell length c length_c	241.740 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	48

Space group space_group	P 63
Space-group number int_tables_number	173
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	49.120 Å
R factor r_factor	0.1910
R_work r_work	0.1900
R_free r_free	0.2140

fit	/app/data/saxs_computation/mf/5mfd/5mfd.fit
pddf	/app/data/pr_computation/mf/5mfd/5mfd.pr.out
profile	/app/data/saxs_computation/mf/5mfd/5mfd.dat

Designed armadillo repeat protein YIIIM''6AII in complex with pD_(KR)5

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

Capsid decoration protein,pD_(KR)5

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

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)