SAXSdb — 4gi3

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

KerA

OrganismNot specified

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 37–310	Not recorded	Greglin × 1 （P85064）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.68M sodium citrate, 0.36M sodium formate, 0.066M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.75 Å R-free 0.201

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 4GI3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4HX2 Crystal structure of Streptomyces caespitosus sermetstatin in complex with Bacillus licheniformis subtilisin Deposited 2012-11-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 37–310（274 aa） Fragment：Mature protease Chain C 37–310（274 aa） Fragment：Mature protease	Not recorded	CA CALCIUM ION × 4 ZN ZINC ION × 2 CL CHLORIDE ION × 1 1AX (2R,2'R)-3,3'-oxydipropane-1,2-diol × 1 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 2 IPA ISOPROPYL ALCOHOL × 3 K POTASSIUM ION × 2 CAC CACODYLATE ION × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；0.1 M cacodylate, 0.2 M zinc acetate dihydrate, 10% (v/v) 2-propanol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.25 Å R-free 0.217
6DWQ Subtilisin serine protease modified with the protease inhibitor cyanobenzylsulfonylfluoride Deposited 2018-06-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 37–310（274 aa） Fragment：residues 37-310	Non-standard monomer：Yes (specific site not provided by mmCIF)	EDO 1,2-ETHANEDIOL × 12 NO3 NITRATE ION × 2 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；26% PEG 3350, 0.350 M NH4NO3	Resolution 1.27 Å R-free 0.148

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

View Construct and Data Evidence

UniProt name	Q9FDF2_BACLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–275； UniProt 37–310

Greglin

OrganismNot specified

UniProt P85064

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 C； UniProt 1–83	Not recorded	KerA × 1 （Q9FDF2）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.68M sodium citrate, 0.36M sodium formate, 0.066M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.75 Å R-free 0.201

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	SPI_SCHGR
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–83； UniProt 1–83

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	4gi3
Deposition date deposition_date	2012-08-08
Structure title title	Crystal structure of Greglin in complex with subtilisin
Keywords keywords	Kazal type inhibitor, HYDROLASE-HYDROLASE INHIBITOR complex; HYDROLASE/HYDROLASE INHIBITOR
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	19.67 Å
Radius of gyration Rg (electron density) rg_electron	18.57 Å
Forward intensity I(0) i0	20669100.00
Molecular weight molecular_weight	33659.0 kDa
Excluded volume excluded_volume	41720 Å³
Envelope volume envelope_volume	46540 Å³
Hydration-shell volume shell_volume	20653 Å³
Envelope diameter envelope_diameter	68.7 Å
Shell Rg shell_rg	25.38 Å
Envelope Rg envelope_rg	18.94 Å
Shape Rg shape_rg	18.57 Å
Total Rg total_rg	19.49 Å
Total atoms total_atoms	2361
Residues n_residues	331
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	69.1 Å
Rg (real space) rg_real	19.57 Å
Rg uncertainty (real space) rg_real_error	0.46 Å
I(0) (real space) i0_real	2.0670e+07
I(0) uncertainty (real space) i0_real_error	2.9460e+05
Rg (reciprocal space) rg_reciprocal	19.59 Å
I(0) (reciprocal space) i0_reciprocal	20670000.0000
Solution quality estimate total_estimate	0.8473
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.3 Å
Skewness Skewness skewness	0.262
Kurtosis Kurtosis kurtosis	-0.182
Angular range angular_range	— – 0.4050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7134000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.676; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.999

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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	KerA
Molecular weight formula_weight	27437.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2729

MAQTVPYGIPLIKADKVQAQGFKGANVKVAVLDTGIQASHPDLNVVGGASFVAGEAYNTDGNGHGTHVAGTVAALDNTTGVLGVAPSVSLYAVKVLNSSGSGSYSGIVSGIEWATTNGMDVINMSLGGASGSTAMKQAVDNAYARGVVVVAAAGNSGSSGNTNTIGYPAKYDSVIAVGAVDSNSNRASFSSVGAELEVMAPGAGVYSTYPTNTYATLNGTSMASPHVAGAAALILSKHPNLSASQVRNRLSSTATYLGSSFYYGKGLINVEAAAQ

Entity 2 Entity 2 polymer

Description description	Greglin
Molecular weight formula_weight	9200.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

SEDDGSASPESQEMSYTELPCPSICPLIYAPVCVEDSNQDFYLFVNECEVRKCGCEAGFVYTFVPREMCKATTSLCPMQTKSS

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	368

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d4gi3a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.41 — Subtilisin-like
Superfamily Superfamily superfamily	c.41.1 — Subtilisin-like
Family Family family	c.41.1.1 — Subtilases

CATH v4.4 (2 domains)

Domain ID domain_id	4gi3A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	200 — Peptidase S8/S53 domain

Domain ID domain_id	4gi3C00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	30 —

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8. Citations (1)

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Unit-cell length a length_a	131.070 Å
Unit-cell length b length_b	39.708 Å
Unit-cell length c length_c	59.750 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	98.05 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.750 Å
Low-resolution limit resolution_low	32.570 Å
R factor r_factor	0.1679
R_work r_work	0.1660
R_free r_free	0.2007

fit	/app/data/saxs_computation/gi/4gi3/4gi3.fit
pddf	/app/data/pr_computation/gi/4gi3/4gi3.pr.out
profile	/app/data/saxs_computation/gi/4gi3/4gi3.dat

Crystal structure of Greglin in complex with subtilisin

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

KerA

State in the Current Structure

Other States of the Same Protein in the Database

Greglin

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

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)