SAXSdb — 3lq0

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

ProAstacin

Astacus astacus

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 16–250	Mutation：I91L,E93A	ZN ZINC ION × 1 GOL GLYCEROL × 3 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；For crystallization, reservoir solutions were prepared by a Tecan robot and 200-nL crystallization drops were dispensed on 96x2-well MRC plates (Innovadyne) by a Cartesian (Genomic Solutions) nanodrop robot at the High-Throughput Crystallography Platform of the Barcelona Science Park. Best crystals appeared in a Bruker steady-temperature crystal farm at 4C with protein solution (10 mg/mL in 50mM AMPSO pH9.0) and 20% PEG 8000, 0.1M (NH4)2SO4, 0.01M MgCl2, 0.05M MES pH5.6 as reservoir solution. These conditions were efficiently scaled up to the microliter range with 24-well Cryschem crystallization dishes (Hampton Research). Crystals were cryo-protected with 16% PEG 8000, 20% glycerol, 0.1M (NH4)2SO4, 0.01M MgCl2, 0.05M MES pH5.6. , VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.45 Å R-free 0.180

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 3LQ0	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AST STRUCTURE OF ASTACIN AND IMPLICATIONS FOR ACTIVATION OF ASTACINS AND ZINC-LIGATION OF COLLAGENASES Deposited 1993-04-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 50–249（200 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å
1IAA CRYSTAL STRUCTURES, SPECTROSCOPIC FEATURES, AND CATALYTIC PROPERTIES OF COBALT(II), COPPER(II), NICKEL(II), AND MERCURY(II) DERIVATIVES OF THE ZINC ENDOPEPTIDASE ASTACIN. A CORRELATION OF STRUCTURE AND PROTEOLYTIC ACTIVITY Deposited 1994-05-09	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 50–249（200 aa）	Not recorded	CU COPPER (II) ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å
1IAB CRYSTAL STRUCTURES, SPECTROSCOPIC FEATURES, AND CATALYTIC PROPERTIES OF COBALT(II), COPPER(II), NICKEL(II), AND MERCURY(II) DERIVATIVES OF THE ZINC ENDOPEPTIDASE ASTACIN. A CORRELATION OF STRUCTURE AND PROTEOLYTIC ACTIVITY Deposited 1994-05-09	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 50–249（200 aa）	Not recorded	CO COBALT (II) ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.79 Å
1IAC REFINED 1.8 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF ASTACIN, A ZINC-ENDOPEPTIDASE FROM THE CRAYFISH ASTACUS ASTACUS L. STRUCTURE DETERMINATION, REFINEMENT, MOLECULAR STRUCTURE AND COMPARISON WITH THERMOLYSIN Deposited 1994-05-09	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 50–249（200 aa）	Not recorded	HG MERCURY (II) ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.10 Å
1IAD REFINED 1.8 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF ASTACIN, A ZINC-ENDOPEPTIDASE FROM THE CRAYFISH ASTACUS ASTACUS L. STRUCTURE DETERMINATION, REFINEMENT, MOLECULAR STRUCTURE AND COMPARISON TO THERMOLYSIN Deposited 1994-05-09	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 50–249（200 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
1IAE CRYSTAL STRUCTURES, SPECTROSCOPIC FEATURES, AND CATALYTIC PROPERTIES OF COBALT(II), COPPER(II), NICKEL(II), AND MERCURY(II) DERIVATIVES OF THE ZINC ENDOPEPTIDASE ASTACIN. A CORRELATION OF STRUCTURE AND PROTEOLYTIC ACTIVITY Deposited 1994-05-09	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 50–249（200 aa）	Not recorded	NI NICKEL (II) ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.83 Å
1QJI Structure of astacin with a transition-state analogue inhibitor Deposited 1999-06-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 50–249（200 aa） Fragment：CATALYTIC DOMAIN	Not recorded	ZN ZINC ION × 1 PKF CARBOBENZOXY-PRO-LYS-PHE-Y(PO2)-ALA-PRO-OME × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；HANGING DROP VAPOUR DIFFUSION PH 7.0, 1M AMMONIUM SULFATE	Resolution 2.14 Å
1QJJ Structure of astacin with a hydroxamic acid inhibitor Deposited 1999-06-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 50–249（200 aa） Fragment：CATALYTIC DOMAIN	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；HANGING DROP VAPOUR DIFFUSION PH 7.0, 1M AMMONIUM SULFATE	Resolution 1.86 Å
6HT9 Mouse fetuin-B in complex with crayfish astacin Deposited 2018-10-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–251（251 aa）	Not recorded	ZN ZINC ION × 1 GOL GLYCEROL × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；ammonium sulfate, polyethylene glycol 2000, sodium acetate, pH 4.6.	Resolution 3.10 Å R-free 0.270
6HT9 Mouse fetuin-B in complex with crayfish astacin Deposited 2018-10-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–251（251 aa）	Not recorded	ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；ammonium sulfate, polyethylene glycol 2000, sodium acetate, pH 4.6.	Resolution 3.10 Å R-free 0.270
6SAZ Cleaved human fetuin-b in complex with crayfish astacin Deposited 2019-07-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 50–251（202 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Crystallization assays were set up following the sitting-drop vapor diffusion method at the joint IBMB/IRB Automated Crystallography Platform of Barcelona Science Park. A Tecan robot (Tecan Trading) was used to prepare reservoir solutions, and a Cartesian Microsys 4000 XL robot (Genomic Solutions) or a Phoenix nanodrop robot (Art Robbins Instruments) dispensed nanocrystallization drops on 96x2-well Swissci Polystyrene MRC Crystallization Plates (Molecular Dimensions). Plates were stored at 4 or 20 degrees in thermostatic crystal farms (Bruker AXS). The astacin-hFB complex only crystallized after incubating the inhibitor (at 7.5 mg/mL) with six-fold molar excess of the peptidase in 10 mM Tris-HCl, 140 mM sodium chloride, pH 6.8. Crystals were obtained at 20 degrees in 200 nL:100 nL drops with protein complex solution and 20 percent (w/v) polyethylene glycol 3,350, 0.2 M sodium tartrate dibasic as reservoir solution.	Resolution 3.00 Å R-free 0.247
6SAZ Cleaved human fetuin-b in complex with crayfish astacin Deposited 2019-07-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 50–251（202 aa）	Not recorded	ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Crystallization assays were set up following the sitting-drop vapor diffusion method at the joint IBMB/IRB Automated Crystallography Platform of Barcelona Science Park. A Tecan robot (Tecan Trading) was used to prepare reservoir solutions, and a Cartesian Microsys 4000 XL robot (Genomic Solutions) or a Phoenix nanodrop robot (Art Robbins Instruments) dispensed nanocrystallization drops on 96x2-well Swissci Polystyrene MRC Crystallization Plates (Molecular Dimensions). Plates were stored at 4 or 20 degrees in thermostatic crystal farms (Bruker AXS). The astacin-hFB complex only crystallized after incubating the inhibitor (at 7.5 mg/mL) with six-fold molar excess of the peptidase in 10 mM Tris-HCl, 140 mM sodium chloride, pH 6.8. Crystals were obtained at 20 degrees in 200 nL:100 nL drops with protein complex solution and 20 percent (w/v) polyethylene glycol 3,350, 0.2 M sodium tartrate dibasic as reservoir solution.	Resolution 3.00 Å R-free 0.247

10 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ASTA_ASTFL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–235； UniProt 16–250

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	3lq0
Deposition date deposition_date	2010-02-08
Structure title title	Zymogen structure of crayfish astacin metallopeptidase
Keywords keywords	metallopeptidase, zymogen activation, proenzyme, protease, Disulfide bond, Hydrolase, Metal-binding, Metalloprotease, Zymogen; HYDROLASE
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	18.08 Å
Radius of gyration Rg (electron density) rg_electron	17.00 Å
Forward intensity I(0) i0	13671800.00
Molecular weight molecular_weight	26824.0 kDa
Excluded volume excluded_volume	33096 Å³
Envelope volume envelope_volume	36965 Å³
Hydration-shell volume shell_volume	17923 Å³
Envelope diameter envelope_diameter	59.1 Å
Shell Rg shell_rg	23.54 Å
Envelope Rg envelope_rg	17.34 Å
Shape Rg shape_rg	16.99 Å
Total Rg total_rg	17.99 Å
Total atoms total_atoms	1883
Residues n_residues	235
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	58.3 Å
Rg (real space) rg_real	17.96 Å
Rg uncertainty (real space) rg_real_error	0.34 Å
I(0) (real space) i0_real	1.3670e+07
I(0) uncertainty (real space) i0_real_error	1.5470e+05
Rg (reciprocal space) rg_reciprocal	17.97 Å
I(0) (reciprocal space) i0_reciprocal	13670000.0000
Solution quality estimate total_estimate	0.8077
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.9 Å
Skewness Skewness skewness	0.197
Kurtosis Kurtosis kurtosis	-0.343
Angular range angular_range	— – 0.4400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3705000.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.835; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.000

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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	ProAstacin
Molecular weight formula_weight	26437.4 kDa
EC 编号 ec_number	3.4.24.21
Mutation mutation	I91L,E93A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2252

SPIIPEAARALYYNDGMFEGDIKLRAGRQPARVGAAILGDEYLWSGGVIPYTFAGVSGADQSAILSGMQELEEKTCIRFVPRTTESDYVEIFTSGSGCWSYVGRISGAQQVSLQANGCVYHGTILHALMHAIGFYHEHTRMDRDNYVTINYQNVDPSMTSNFDIDTYSRYVGEDYQYYSIMHYGKYSFSIQWGVLETIVPLQNGIDLTDPYDKAHMLQTDANQINNLYTNECSLR

来源 Source

来源生物 organism	Astacus astacus
通用名 common_name	Broad-fingered crayfish
NCBI Class编号 ncbi_taxonomy_id	6715
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	298

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	3lq0A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	390 — Collagenase (Catalytic Domain)
Homologous superfamily homologous superfamily	10 — Collagenase (Catalytic Domain)

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8. Citations (1)

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Unit-cell length a length_a	55.910 Å
Unit-cell length b length_b	63.370 Å
Unit-cell length c length_c	69.190 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	4

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

Resolution resolution	1.450 Å
Low-resolution limit resolution_low	41.920 Å
R factor r_factor	0.1522
R_work r_work	0.1517
R_free r_free	0.1805

fit	/app/data/saxs_computation/lq/3lq0/3lq0.fit
pddf	/app/data/pr_computation/lq/3lq0/3lq0.pr.out
profile	/app/data/saxs_computation/lq/3lq0/3lq0.dat

Zymogen structure of crayfish astacin metallopeptidase

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

ProAstacin

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