SAXSdb — 1y55

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

Avidin-related protein 4/5

Gallus gallus

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 homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain X； UniProt 25–150 Chain Y； UniProt 25–150	Mutation：C122S	BTN BIOTIN × 4 FMT FORMIC ACID × 8	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.2；293 K；2M sodium formate, 0.1M sodium acetate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.00 Å R-free 0.177

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 1Y55	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1Y52 structure of insect cell (Baculovirus) expressed AVR4 (C122S)-biotin complex Deposited 2004-12-02	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain X 25–150（126 aa） Chain Y 25–150（126 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 BTN BIOTIN × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；2.0M ammonium sulfate,0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.70 Å R-free 0.200
1Y53 Crystal structure of bacterial expressed avidin related protein 4 (AVR4) C122S Deposited 2004-12-02	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain X 25–150（126 aa） Chain Y 25–150（126 aa）	Mutation：C122S Mutation：C122S	FMT FORMIC ACID × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.2；293 K；2M sodium formate, 0.1M sodium acetate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.20 Å R-free 0.185
2FHL avidin related protein (AVR4)-BNA complex Deposited 2005-12-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 25–145（121 aa） Chain B 25–145（121 aa）	Mutation：C122S Mutation：C122S	BNI 5-(2-OXO-HEXAHYDRO-THIENO[3,4-D]IMIDAZOL-6-YL)-PENTANOIC ACID (4-NITRO-PHENYL)-AMIDE × 4 FMT FORMIC ACID × 20	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；3.0M format, 0.1 M acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.05 Å R-free 0.177
2FHN Avidin related protein AVR4 (C122S, K109I mutant) in complex with BNA Deposited 2005-12-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain X 25–145（121 aa） Chain Y 25–145（121 aa）	Mutation：C122S,K109I Mutation：C122S,K109I	BNI 5-(2-OXO-HEXAHYDRO-THIENO[3,4-D]IMIDAZOL-6-YL)-PENTANOIC ACID (4-NITRO-PHENYL)-AMIDE × 4 FMT FORMIC ACID × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；3. M farmat, 0.1M acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.30 Å R-free 0.166
2MF6 Solution NMR structure of Chimeric Avidin, ChiAVD(I117Y), in the biotin bound form Deposited 2013-10-07	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 Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 62–82（21 aa） Fragment：P02701 Residues 25-61, 85-152 and P56734 residues 62-82 Chain B 62–82（21 aa） Fragment：P02701 Residues 25-61, 85-152 and P56734 residues 62-82 Chain C 62–82（21 aa） Fragment：P02701 Residues 25-61, 85-152 and P56734 residues 62-82 Chain D 62–82（21 aa） Fragment：P02701 Residues 25-61, 85-152 and P56734 residues 62-82	Mutation：I117Y Mutation：I117Y Mutation：I117Y Mutation：I117Y	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；333 K；Pressure 1 NMR measurement conditions pH 6.5；333 K；Pressure 1 NMR sample composition 0.7-1.2 mM [U-13C; U-15N] avidin-1, 0.7-1.2 mM d-biotin-2, 93 % H2O-3, 7 % D2O-4, 93% H2O/7% D2O \| 93% H2O/7% D2O NMR sample composition 0.7-1.2 mM [U-13C; U-15N] avidin-5, 0.7-1.2 mM d-biotin-6, 100 % D2O-7, 100% D2O \| 100% D2O	Resolution not provided
2OF8 Crystal structure of AVR4 (D39A/C122S)-BNA complex Deposited 2007-01-03	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 25–150（126 aa） Chain B 25–150（126 aa）	Mutation：D39A, C122S, D239A, C322S Mutation：D39A, C122S, D239A, C322S	BNI 5-(2-OXO-HEXAHYDRO-THIENO[3,4-D]IMIDAZOL-6-YL)-PENTANOIC ACID (4-NITRO-PHENYL)-AMIDE × 4 FMT FORMIC ACID × 22	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.2；293 K；1.5-1.9M NaFormat, 0.1M Acetate, PH 4.2-4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.05 Å R-free 0.177
2OF9 Crystal structure of apo AVR4 (D39A/C122S) Deposited 2007-01-03	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 25–150（126 aa） Chain B 25–150（126 aa）	Mutation：D39A, C122S, D239A, C322S Mutation：D39A, C122S, D239A, C322S	FMT FORMIC ACID × 30	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；1.5-1.9M NaFormate, 0.1M Acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.35 Å R-free 0.192
2OFA Crystal structure of apo AVR4 (R112L,C122S) Deposited 2007-01-03	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 25–150（126 aa） Chain B 25–150（126 aa）	Mutation：R112L, C122S, R312L, C322S Mutation：R112L, C122S, R312L, C322S	FMT FORMIC ACID × 16	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.4；293 K；1.5-1.9M NaFormate, 0.1M Acetate, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.50 Å R-free 0.188
2OFB Crystal structure of AVR4 (R112L/C122S)-BNA complex Deposited 2007-01-03	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 25–150（126 aa） Chain B 25–150（126 aa）	Mutation：R112L, C122S, R312L, C322S Mutation：R112L, C122S, R312L, C322S	BNI 5-(2-OXO-HEXAHYDRO-THIENO[3,4-D]IMIDAZOL-6-YL)-PENTANOIC ACID (4-NITRO-PHENYL)-AMIDE × 4 FMT FORMIC ACID × 16	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；1.5-1.9M NaFormate, 0.1M Acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.16 Å R-free 0.187
3MM0 Crystal structure of chimeric avidin Deposited 2010-04-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 62–82（21 aa） Fragment：P02701 Residues 25-61, 85-152 and P56734 residues 62-82 Chain B 62–82（21 aa） Fragment：P02701 Residues 25-61, 85-152 and P56734 residues 62-82 Chain C 62–82（21 aa） Fragment：P02701 Residues 25-61, 85-152 and P56734 residues 62-82 Chain D 62–82（21 aa） Fragment：P02701 Residues 25-61, 85-152 and P56734 residues 62-82	Mutation：I141Y Mutation：I141Y Mutation：I141Y Mutation：I141Y	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH；pH 8.3；293 K；20% Polyethylene glycol monomethyl ether 5000, 0.1M Tris (pH 8.3), and 9mM ammonium sulfate, microbatch, temperature 293K	Resolution 2.70 Å R-free 0.309
3MM0 Crystal structure of chimeric avidin Deposited 2010-04-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain E 62–82（21 aa） Fragment：P02701 Residues 25-61, 85-152 and P56734 residues 62-82 Chain F 62–82（21 aa） Fragment：P02701 Residues 25-61, 85-152 and P56734 residues 62-82 Chain G 62–82（21 aa） Fragment：P02701 Residues 25-61, 85-152 and P56734 residues 62-82 Chain H 62–82（21 aa） Fragment：P02701 Residues 25-61, 85-152 and P56734 residues 62-82	Mutation：I141Y Mutation：I141Y Mutation：I141Y Mutation：I141Y	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH；pH 8.3；293 K；20% Polyethylene glycol monomethyl ether 5000, 0.1M Tris (pH 8.3), and 9mM ammonium sulfate, microbatch, temperature 293K	Resolution 2.70 Å R-free 0.309
3MM0 Crystal structure of chimeric avidin Deposited 2010-04-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Insufficient information Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain I 62–82（21 aa） Fragment：P02701 Residues 25-61, 85-152 and P56734 residues 62-82 Chain K 62–82（21 aa） Fragment：P02701 Residues 25-61, 85-152 and P56734 residues 62-82	Mutation：I141Y Mutation：I141Y	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH；pH 8.3；293 K；20% Polyethylene glycol monomethyl ether 5000, 0.1M Tris (pH 8.3), and 9mM ammonium sulfate, microbatch, temperature 293K	Resolution 2.70 Å R-free 0.309
3MM0 Crystal structure of chimeric avidin Deposited 2010-04-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Insufficient information Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain M 62–82（21 aa） Fragment：P02701 Residues 25-61, 85-152 and P56734 residues 62-82 Chain N 62–82（21 aa） Fragment：P02701 Residues 25-61, 85-152 and P56734 residues 62-82	Mutation：I141Y Mutation：I141Y	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH；pH 8.3；293 K；20% Polyethylene glycol monomethyl ether 5000, 0.1M Tris (pH 8.3), and 9mM ammonium sulfate, microbatch, temperature 293K	Resolution 2.70 Å R-free 0.309

10 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	AVR4_CHICK
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain X； PDBConstruct 1–126； UniProt 25–150 Author chain Y； PDBConstruct 1–126； UniProt 25–150

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	1y55
Deposition date deposition_date	2004-12-02
Structure title title	Crystal structure of the C122S mutant of E. Coli expressed avidin related protein 4 (AVR4)-biotin complex
Keywords keywords	avidin, streptavidin, biotin, avidin related molecule, high affinity, thermostability, SUGAR BINDING PROTEIN; SUGAR BINDING 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	18.40 Å
Radius of gyration Rg (electron density) rg_electron	17.24 Å
Forward intensity I(0) i0	13757300.00
Molecular weight molecular_weight	27533.0 kDa
Excluded volume excluded_volume	34329 Å³
Envelope volume envelope_volume	38391 Å³
Hydration-shell volume shell_volume	18249 Å³
Envelope diameter envelope_diameter	66.1 Å
Shell Rg shell_rg	23.91 Å
Envelope Rg envelope_rg	17.81 Å
Shape Rg shape_rg	17.21 Å
Total Rg total_rg	18.31 Å
Total atoms total_atoms	1938
Residues n_residues	240
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	67.1 Å
Rg (real space) rg_real	18.33 Å
Rg uncertainty (real space) rg_real_error	0.46 Å
I(0) (real space) i0_real	1.3760e+07
I(0) uncertainty (real space) i0_real_error	1.8290e+05
Rg (reciprocal space) rg_reciprocal	18.34 Å
I(0) (reciprocal space) i0_reciprocal	13760000.0000
Solution quality estimate total_estimate	0.8329
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.1 Å
Skewness Skewness skewness	0.284
Kurtosis Kurtosis kurtosis	-0.167
Angular range angular_range	— – 0.4300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4395000.0000
Real-space data points n_real_points	74
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.617; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.998

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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	Avidin-related protein 4/5
Molecular weight formula_weight	14158.9 kDa
Mutation mutation	C122S
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	X,Y
Atom count atom_count	2260

ARKCSLTGKWTNNLGSIMTIRAVNSRGEFTGTYLTAVADNPGNITLSPLLGIQHKRASQPTFGFTVHWNFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDISYDWKATRVGYNNFTRLSTVEE

来源 Source

来源生物 organism	Gallus gallus
通用名 common_name	chicken
NCBI Class编号 ncbi_taxonomy_id	9031
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	BIOTIN
Molecular weight formula_weight	244.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	FORMIC ACID
Molecular weight formula_weight	46.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	240

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1y55x1
Class class	b — All beta proteins
Fold Fold fold	b.61 — Streptavidin-like
Superfamily Superfamily superfamily	b.61.1 — Avidin/streptavidin
Family Family family	b.61.1.1 — Avidin/streptavidin

Domain ID domain_id	d1y55x2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1y55y1
Class class	b — All beta proteins
Fold Fold fold	b.61 — Streptavidin-like
Superfamily Superfamily superfamily	b.61.1 — Avidin/streptavidin
Family Family family	b.61.1.1 — Avidin/streptavidin

Domain ID domain_id	d1y55y2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id	1y55X00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	30 — Avidin-like

Domain ID domain_id	1y55Y00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	30 — Avidin-like

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8. Citations (1)

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Unit-cell length a length_a	78.173 Å
Unit-cell length b length_b	78.173 Å
Unit-cell length c length_c	110.260 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	16

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	1.000 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.1657
R_work r_work	0.1651
R_free r_free	0.1766

fit	/app/data/saxs_computation/y5/1y55/1y55.fit
pddf	/app/data/pr_computation/y5/1y55/1y55.pr.out
profile	/app/data/saxs_computation/y5/1y55/1y55.dat

Crystal structure of the C122S mutant of E. Coli expressed avidin related protein 4 (AVR4)-biotin complex

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

Avidin-related protein 4/5

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