SAXSdb — 4jph

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

Gremlin-2

Mus musculus

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 22–168 Chain B； UniProt 22–168	Fragment：UNP residues 22-168	GOL GLYCEROL × 8 GSH Glutathione × 2 CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；295 K；PEG3350, sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.25 Å R-free 0.222
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 22–168 Chain D； UniProt 22–168	Fragment：UNP residues 22-168	GOL GLYCEROL × 4 GSH Glutathione × 2 CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；295 K；PEG3350, sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.25 Å R-free 0.222

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 4JPH	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5HK5 Structure of the Grem2-GDF5 Inhibitory Complex Deposited 2016-01-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 22–168（147 aa） Chain F 22–168（147 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；HEPES, ammonium chloride, ethylammonium nitrate	Resolution 2.90 Å R-free 0.282
5HK5 Structure of the Grem2-GDF5 Inhibitory Complex Deposited 2016-01-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 22–168（147 aa） Chain F 22–168（147 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；HEPES, ammonium chloride, ethylammonium nitrate	Resolution 2.90 Å R-free 0.282
5HK5 Structure of the Grem2-GDF5 Inhibitory Complex Deposited 2016-01-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain G 22–168（147 aa） Chain H 22–168（147 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；HEPES, ammonium chloride, ethylammonium nitrate	Resolution 2.90 Å R-free 0.282
5HK5 Structure of the Grem2-GDF5 Inhibitory Complex Deposited 2016-01-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain G 22–168（147 aa） Chain H 22–168（147 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；HEPES, ammonium chloride, ethylammonium nitrate	Resolution 2.90 Å R-free 0.282

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

View Construct and Data Evidence

UniProt name	GREM2_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–148； UniProt 22–168 Author chain B； PDBConstruct 2–148； UniProt 22–168 Author chain C； PDBConstruct 2–148； UniProt 22–168 Author chain D； PDBConstruct 2–148； UniProt 22–168

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	4jph
Deposition date deposition_date	2013-03-19
Structure title title	Crystal structure of Protein Related to DAN and Cerberus (PRDC)
Keywords keywords	Cystine knot, DAN domain, CAN domain, BMP antagonist, BMP-2, BMP-4, BMP-7, GDF-5, GSH, extracellular, CYTOKINE; CYTOKINE
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	34.45 Å
Radius of gyration Rg (electron density) rg_electron	33.97 Å
Forward intensity I(0) i0	46085000.00
Molecular weight molecular_weight	51991.0 kDa
Excluded volume excluded_volume	64480 Å³
Envelope volume envelope_volume	99241 Å³
Hydration-shell volume shell_volume	24621 Å³
Envelope diameter envelope_diameter	104.2 Å
Shell Rg shell_rg	40.59 Å
Envelope Rg envelope_rg	32.50 Å
Shape Rg shape_rg	33.99 Å
Total Rg total_rg	34.50 Å
Total atoms total_atoms	3723
Residues n_residues	438
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	103.3 Å
Rg (real space) rg_real	34.41 Å
Rg uncertainty (real space) rg_real_error	0.80 Å
I(0) (real space) i0_real	4.6090e+07
I(0) uncertainty (real space) i0_real_error	7.2700e+05
Rg (reciprocal space) rg_reciprocal	34.44 Å
I(0) (reciprocal space) i0_reciprocal	46090000.0000
Solution quality estimate total_estimate	0.8463
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	58.4 Å
Skewness Skewness skewness	-0.020
Kurtosis Kurtosis kurtosis	-1.028
Angular range angular_range	— – 0.2300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1736000.0000
Real-space data points n_real_points	47
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.763; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.834; Smooth: 0.876

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Gremlin-2
Molecular weight formula_weight	17138.7 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	3854

MRKNRPAGAIPSPYKDGSSNNSERWHHQIKEVLASSQEALVVTERKYLKSDWCKTQPLRQTVSEEGCRSRTILNRFCYGQCNSFYIPRHVKKEEDSFQSCAFCKPQRVTSVIVELECPGLDPPFRIKKIQKVKHCRCMSVNLSDSDKQ

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 3 Entity 3 non-polymer

Description description	GLUTATHIONE
Molecular weight formula_weight	307.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	CITRIC ACID
Molecular weight formula_weight	192.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	113

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	4jphB00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	90 — Cystine Knot Cytokines, subunit B
Homologous superfamily homologous superfamily	10 — Cystine-knot cytokines

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8. Citations (1)

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Unit-cell length a length_a	73.312 Å
Unit-cell length b length_b	65.558 Å
Unit-cell length c length_c	85.077 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	105.50 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.250 Å
Low-resolution limit resolution_low	17.600 Å
R factor r_factor	0.2034
R_work r_work	0.2023
R_free r_free	0.2224

fit	/app/data/saxs_computation/jp/4jph/4jph.fit
pddf	/app/data/pr_computation/jp/4jph/4jph.pr.out
profile	/app/data/saxs_computation/jp/4jph/4jph.dat

Crystal structure of Protein Related to DAN and Cerberus (PRDC)

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

Gremlin-2

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