SAXSdb — 2qc7

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

Endoplasmic reticulum protein ERp29

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 34–261	Not recorded	No other associated polymer	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
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 34–261	Not recorded	No other associated polymer	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

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 2QC7	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5V8Z Crystal structure of ERp29 D-domain in complex with the P-domain of calmegin Deposited 2017-03-22	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 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；1.4 M sodium citrate pH 7.5	Resolution 2.10 Å R-free 0.219
5V8Z Crystal structure of ERp29 D-domain in complex with the P-domain of calmegin Deposited 2017-03-22	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 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；1.4 M sodium citrate pH 7.5	Resolution 2.10 Å R-free 0.219
5V90 Crystal structure of ERp29 D-domain in complex with the P-domain of calreticulin Deposited 2017-03-22	Different construct Different oligomeric state 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 construct Different oligomeric state 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 3–230； UniProt 34–261 Author chain B； PDBConstruct 3–230； UniProt 34–261

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	2qc7
Deposition date deposition_date	2007-06-19
Structure title title	Crystal structure of the protein-disulfide isomerase related chaperone ERp29
Keywords keywords	b domain (residues 33-153), D domain (residues 154-261), CHAPERONE; 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	31.85 Å
Radius of gyration Rg (electron density) rg_electron	31.42 Å
Forward intensity I(0) i0	38055400.00
Molecular weight molecular_weight	50001.0 kDa
Excluded volume excluded_volume	63292 Å³
Envelope volume envelope_volume	87780 Å³
Hydration-shell volume shell_volume	24618 Å³
Envelope diameter envelope_diameter	105.2 Å
Shell Rg shell_rg	36.51 Å
Envelope Rg envelope_rg	30.63 Å
Shape Rg shape_rg	31.40 Å
Total Rg total_rg	31.98 Å
Total atoms total_atoms	3526
Residues n_residues	448
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	102.8 Å
Rg (real space) rg_real	31.97 Å
Rg uncertainty (real space) rg_real_error	1.12 Å
I(0) (real space) i0_real	3.8060e+07
I(0) uncertainty (real space) i0_real_error	6.1440e+05
Rg (reciprocal space) rg_reciprocal	31.93 Å
I(0) (reciprocal space) i0_reciprocal	38050000.0000
Solution quality estimate total_estimate	0.8765
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	22.6 Å
Skewness Skewness skewness	0.265
Kurtosis Kurtosis kurtosis	-0.743
Angular range angular_range	— – 0.2500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5937000.0000
Real-space data points n_real_points	51
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.903; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.830; Smooth: 0.863

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	2qc7A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	10 — Glutaredoxin

Domain ID domain_id	2qc7A02
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	2qc7B01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	10 — Glutaredoxin

Domain ID domain_id	2qc7B02
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	58.044 Å
Unit-cell length b length_b	68.025 Å
Unit-cell length c length_c	70.088 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	107.46 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 2 1
Space-group number int_tables_number	3
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	28.980 Å
R factor r_factor	0.2650
R_work r_work	0.2650
R_free r_free	0.2790

Description description	Endoplasmic reticulum protein ERp29
Molecular weight formula_weight	27222.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3526

Crystal structure of the protein-disulfide isomerase related chaperone ERp29

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

Endoplasmic reticulum protein ERp29

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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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

fit	/app/data/saxs_computation/qc/2qc7/2qc7.fit
pddf	/app/data/pr_computation/qc/2qc7/2qc7.pr.out
profile	/app/data/saxs_computation/qc/2qc7/2qc7.dat