1cxv

STRUCTURE OF RECOMBINANT MOUSE COLLAGENASE-3 (MMP-13)

Method: X-RAY DIFFRACTION Dmax: 69.7 Å Quality: EXCELLENT

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

PROTEIN (COLLAGENASE-3)

OrganismNot specified

UniProt P33435

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 105–268 Fragment:CATALYTIC DOMAIN ZN ZINC ION × 2 CA CALCIUM ION × 2 CBP 2-{4-[4-(4-CHLORO-PHENOXY)-BENZENESULFONYL]-TETRAHYDRO-PYRAN-4-YL}-N-HYDROXY-ACETAMIDE × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.00 Å R-free 0.234
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 105–268 Fragment:CATALYTIC DOMAIN ZN ZINC ION × 2 CA CALCIUM ION × 2 CBP 2-{4-[4-(4-CHLORO-PHENOXY)-BENZENESULFONYL]-TETRAHYDRO-PYRAN-4-YL}-N-HYDROXY-ACETAMIDE × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.00 Å R-free 0.234

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 MMP13_MOUSE
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–164; UniProt 105–268 Author chain B; PDBConstruct 1–164; UniProt 105–268

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.

SAXS scattering curve SAXS Profile

SAXS profile for 1cxv

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1cxv
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1cxv
Deposition date deposition_date1999-08-30
Structure title titleSTRUCTURE OF RECOMBINANT MOUSE COLLAGENASE-3 (MMP-13)
Keywords keywordsMETALLOPROTEASE, GLYCOPROTEIN, COLLAGEN DEGRADATION, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier21.94
Radius of gyration Rg (electron density) rg_electron21.24
Forward intensity I(0) i023543700.00
Molecular weight molecular_weight37438.0 kDa
Excluded volume excluded_volume46669 ų
Envelope volume envelope_volume53828 ų
Hydration-shell volume shell_volume21376 ų
Envelope diameter envelope_diameter70.5
Shell Rg shell_rg27.37
Envelope Rg envelope_rg21.32
Shape Rg shape_rg21.21
Total Rg total_rg22.10
Total atoms total_atoms2632
Residues n_residues320
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax69.7
Rg (real space) rg_real21.91
Rg uncertainty (real space) rg_real_error0.41
I(0) (real space) i0_real2.3540e+07
I(0) uncertainty (real space) i0_real_error3.1710e+05
Rg (reciprocal space) rg_reciprocal21.92
I(0) (reciprocal space) i0_reciprocal23540000.0000
Solution quality estimate total_estimate0.9013
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary23.9
Skewness Skewness skewness0.307
Kurtosis Kurtosis kurtosis-0.465
Angular range angular_range— – 0.3600 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4871000.0000
Real-space data points n_real_points68
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.908; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.999

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1cxva_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.92 — Zincin-like
Superfamily Superfamily superfamilyd.92.1 — Metalloproteases ('zincins'), catalytic domain
Family Family familyd.92.1.11 — Matrix metalloproteases, catalytic domain
Domain ID domain_idd1cxvb_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.92 — Zincin-like
Superfamily Superfamily superfamilyd.92.1 — Metalloproteases ('zincins'), catalytic domain
Family Family familyd.92.1.11 — Matrix metalloproteases, catalytic domain

CATH v4.4 (2 domains)

Domain ID domain_id1cxvA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology390 — Collagenase (Catalytic Domain)
Homologous superfamily homologous superfamily10 — Collagenase (Catalytic Domain)
Domain ID domain_id1cxvB00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology390 — Collagenase (Catalytic Domain)
Homologous superfamily homologous superfamily10 — Collagenase (Catalytic Domain)

8. Citations (3)

9. Files and Curves (10)