SAXSdb — 5v8z

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

Endoplasmic reticulum resident protein 29

Homo sapiens

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 158–261	Fragment：UNP residues 158-261	Calmegin × 1 （E2RA18）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；1.4 M sodium citrate pH 7.5	Resolution 2.10 Å R-free 0.219
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 158–261	Fragment：UNP residues 158-261	Calmegin × 1 （E2RA18）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；1.4 M sodium citrate pH 7.5	Resolution 2.10 Å R-free 0.219

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 5V8Z	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2QC7 Crystal structure of the protein-disulfide isomerase related chaperone ERp29 Deposited 2007-06-19	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 34–261（228 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；10 mg/ml protein in 5 mM HEPES, pH 7.5, 25 mM NaCl, 0.0025% (v/v) beta-mercaptoethanol was equlibrated with a reservoir containing 0.45 M (NH4)2SO4, 0.1 M sodium acetate buffer, pH 4.5 and 18-20% (w/v) PEG 2000 monomethyl ether. Crystals of about 0.1 mm in size grew in two days. , VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.90 Å R-free 0.279
2QC7 Crystal structure of the protein-disulfide isomerase related chaperone ERp29 Deposited 2007-06-19	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 34–261（228 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；10 mg/ml protein in 5 mM HEPES, pH 7.5, 25 mM NaCl, 0.0025% (v/v) beta-mercaptoethanol was equlibrated with a reservoir containing 0.45 M (NH4)2SO4, 0.1 M sodium acetate buffer, pH 4.5 and 18-20% (w/v) PEG 2000 monomethyl ether. Crystals of about 0.1 mm in size grew in two days. , VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.90 Å R-free 0.279
5V90 Crystal structure of ERp29 D-domain in complex with the P-domain of calreticulin Deposited 2017-03-22	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 158–261（104 aa） Fragment：UNP residues 158-261	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；2.0 M ammonium sulfate, 0.1 M HEPES pH 7.5	Resolution 3.25 Å R-free 0.262
5V90 Crystal structure of ERp29 D-domain in complex with the P-domain of calreticulin Deposited 2017-03-22	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 158–261（104 aa） Fragment：UNP residues 158-261	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；2.0 M ammonium sulfate, 0.1 M HEPES pH 7.5	Resolution 3.25 Å R-free 0.262

2 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ERP29_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–106； UniProt 158–261 Author chain C； PDBConstruct 3–106； UniProt 158–261

Calmegin

Canis lupus familiaris

UniProt E2RA18

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 327–360	Fragment：UNP residues 327-360	Endoplasmic reticulum resident protein 29 × 1 （P30040）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；1.4 M sodium citrate pH 7.5	Resolution 2.10 Å R-free 0.219
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 327–360	Fragment：UNP residues 327-360	Endoplasmic reticulum resident protein 29 × 1 （P30040）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；1.4 M sodium citrate pH 7.5	Resolution 2.10 Å R-free 0.219

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	CLGN_CANLF
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 5–38； UniProt 327–360 Author chain D； PDBConstruct 5–38； UniProt 327–360

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	5v8z
Deposition date deposition_date	2017-03-22
Structure title title	Crystal structure of ERp29 D-domain in complex with the P-domain of calmegin
Keywords keywords	chaperone, protein binding, protein folding; CHAPERONE
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	20.02 Å
Radius of gyration Rg (electron density) rg_electron	19.07 Å
Forward intensity I(0) i0	14518700.00
Molecular weight molecular_weight	28133.0 kDa
Excluded volume excluded_volume	35089 Å³
Envelope volume envelope_volume	42241 Å³
Hydration-shell volume shell_volume	18812 Å³
Envelope diameter envelope_diameter	64.5 Å
Shell Rg shell_rg	25.05 Å
Envelope Rg envelope_rg	19.35 Å
Shape Rg shape_rg	19.07 Å
Total Rg total_rg	19.95 Å
Total atoms total_atoms	1977
Residues n_residues	249
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	62.6 Å
Rg (real space) rg_real	19.92 Å
Rg uncertainty (real space) rg_real_error	0.33 Å
I(0) (real space) i0_real	1.4520e+07
I(0) uncertainty (real space) i0_real_error	1.7700e+05
Rg (reciprocal space) rg_reciprocal	19.94 Å
I(0) (reciprocal space) i0_reciprocal	14520000.0000
Solution quality estimate total_estimate	0.9051
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.9 Å
Skewness Skewness skewness	0.171
Kurtosis Kurtosis kurtosis	-0.456
Angular range angular_range	— – 0.3950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4509000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.925; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.990

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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	Endoplasmic reticulum resident protein 29
Molecular weight formula_weight	11903.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	2014

GSLPVYDALAGEFIRASGVEARQALLKQGQDNLSSVKETQKKWAEQYLKIMGKILDQGEDFPASEMTRIARLIEKNKMSDGKKEELQKSLNILTAFQKKGAEKEEL

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Calmegin
Molecular weight formula_weight	4342.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GSHMDEPKFIPDPNAEKPDDWNEDMDGEWEAPRISNPA

来源 Source

来源生物 organism	Canis lupus familiaris
通用名 common_name	Dog
NCBI Class编号 ncbi_taxonomy_id	9615
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	37

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d5v8za1
Class class	a — All alpha proteins
Fold Fold fold	a.71 — ERP29 C domain-like
Superfamily Superfamily superfamily	a.71.1 — ERP29 C domain-like
Family Family family	a.71.1.1 — ERP29 C domain-like

Domain ID domain_id	d5v8za2
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	d5v8zc1
Class class	a — All alpha proteins
Fold Fold fold	a.71 — ERP29 C domain-like
Superfamily Superfamily superfamily	a.71.1 — ERP29 C domain-like
Family Family family	a.71.1.1 — ERP29 C domain-like

Domain ID domain_id	d5v8zc2
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	5v8zA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1150 — Endoplasmic reticulum protein erp29
Homologous superfamily homologous superfamily	12 — Endoplasmic reticulum resident protein 29, C-terminal domain

Domain ID domain_id	5v8zC00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1150 — Endoplasmic reticulum protein erp29
Homologous superfamily homologous superfamily	12 — Endoplasmic reticulum resident protein 29, C-terminal domain

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8. Citations (1)

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Unit-cell length a length_a	67.782 Å
Unit-cell length b length_b	67.620 Å
Unit-cell length c length_c	73.492 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.105 Å
Low-resolution limit resolution_low	33.810 Å
R factor r_factor	0.2117
R_work r_work	0.2112
R_free r_free	0.2191

fit	/app/data/saxs_computation/v8/5v8z/5v8z.fit
pddf	/app/data/pr_computation/v8/5v8z/5v8z.pr.out
profile	/app/data/saxs_computation/v8/5v8z/5v8z.dat

Crystal structure of ERp29 D-domain in complex with the P-domain of calmegin

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

Endoplasmic reticulum resident protein 29

State in the Current Structure

Other States of the Same Protein in the Database

Calmegin

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)