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- PDB-1qib: CRYSTAL STRUCTURE OF GELATINASE A CATALYTIC DOMAIN -

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Basic information

Entry
Database: PDB / ID: 1qib
TitleCRYSTAL STRUCTURE OF GELATINASE A CATALYTIC DOMAIN
Components72 kDa type IV collagenase
KeywordsHYDROLASE / INHIBITOR / MATRIXIN / MATRIX METALLOPROTEINASE-2 (MMP-2) / GELATINASE A / METZINCIN
Function / homology
Function and homology information


gelatinase A / bone trabecula formation / peripheral nervous system axon regeneration / blood vessel maturation / parturition / luteinization / tissue remodeling / intramembranous ossification / cellular response to UV-A / ovulation from ovarian follicle ...gelatinase A / bone trabecula formation / peripheral nervous system axon regeneration / blood vessel maturation / parturition / luteinization / tissue remodeling / intramembranous ossification / cellular response to UV-A / ovulation from ovarian follicle / positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / prostate gland epithelium morphogenesis / protein metabolic process / cellular response to fluid shear stress / negative regulation of cell adhesion / face morphogenesis / negative regulation of vasoconstriction / macrophage chemotaxis / Activation of Matrix Metalloproteinases / endodermal cell differentiation / response to amyloid-beta / Collagen degradation / fibronectin binding / EPH-ephrin mediated repulsion of cells / collagen catabolic process / extracellular matrix disassembly / response to hyperoxia / ephrin receptor signaling pathway / cellular response to interleukin-1 / response to mechanical stimulus / response to electrical stimulus / response to retinoic acid / ovarian follicle development / embryo implantation / positive regulation of vascular associated smooth muscle cell proliferation / Degradation of the extracellular matrix / extracellular matrix organization / sarcomere / response to activity / response to nicotine / cellular response to estradiol stimulus / cellular response to amino acid stimulus / protein catabolic process / response to hydrogen peroxide / metalloendopeptidase activity / cellular response to reactive oxygen species / response to estrogen / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / metallopeptidase activity / heart development / collagen-containing extracellular matrix / angiogenesis / Interleukin-4 and Interleukin-13 signaling / endopeptidase activity / Extra-nuclear estrogen signaling / response to hypoxia / positive regulation of cell migration / response to xenobiotic stimulus / serine-type endopeptidase activity / mitochondrion / proteolysis / extracellular space / zinc ion binding / extracellular region / nucleus / plasma membrane
Similarity search - Function
Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidase M10A, cysteine switch, zinc binding site ...Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidase M10A, cysteine switch, zinc binding site / Matrixins cysteine switch. / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin / Hemopexin repeat profile. / Hemopexin-like repeats. / Peptidase M10A / Peptidase M10A, catalytic domain / Peptidase M10, metallopeptidase / Matrixin / PGBD-like superfamily / Peptidase, metallopeptidase / Zinc-dependent metalloprotease / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / Kringle-like fold / Neutral zinc metallopeptidases, zinc-binding region signature. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
72 kDa type IV collagenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsDhanaraj, V. / Williams, M.G. / Ye, Q.-Z. / Molina, F. / Johnson, L.L. / Ortwine, D.F. / Pavlovsky, A. / Rubin, J.R. / Skeean, R.W. / White, A.D. ...Dhanaraj, V. / Williams, M.G. / Ye, Q.-Z. / Molina, F. / Johnson, L.L. / Ortwine, D.F. / Pavlovsky, A. / Rubin, J.R. / Skeean, R.W. / White, A.D. / Humblet, C. / Hupe, D.J. / Blundell, T.L.
CitationJournal: Croatica Chemica Acta / Year: 1999
Title: X-ray structure of gelatinase A catalytic domain complexed with a hydroxamate inhibitor
Authors: Dhanaraj, V. / Williams, M.G. / Ye, Q.-Z. / Molina, F. / Johnson, L.L. / Ortwine, D.F. / Pavlovsky, A. / Rubin, J.R. / Skeean, R.W. / White, A.D. / Humblet, C. / Hupe, D.J. / Blundell, T.L.
History
DepositionJun 11, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Nov 19, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 31, 2017Group: Database references / Structure summary
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 72 kDa type IV collagenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2096
Polymers17,9581
Non-polymers2515
Water905
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.830, 84.830, 57.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Cell settingtetragonal
Space group name H-MP4122

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Components

#1: Protein 72 kDa type IV collagenase / E.C.3.4.24.24 / 72 kDa gelatinase / Gelatinase A / Matrix metalloproteinase-2 / MMP-2 / TBE-1


Mass: 17957.861 Da / Num. of mol.: 1
Fragment: CATALYTIC DOMAIN RESIDUES 88-250 WITH THE FIBRONECTIN DOMAIN DELETED
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MMP2, CLG4A / Production host: Escherichia coli (E. coli) / References: UniProt: P08253, gelatinase A
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE WHOLE FIBRONECTIN DOMAIN DELETED AND REPLACED WITH THE SHORT SEGMENT SLGKGV (187-191), ...THE WHOLE FIBRONECTIN DOMAIN DELETED AND REPLACED WITH THE SHORT SEGMENT SLGKGV (187-191), STROMELYSIN NUMBERING

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.57 %
Crystal growpH: 6 / Details: pH 6.0
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
250 mMTris-HCl1drop
30.010 mM1reservoirZnCl2
410 mM1reservoirCaCl2
5PEG80001reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Type: SRS / Wavelength: 0.87
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 5551 / % possible obs: 99.5 % / Redundancy: 6.9 % / Rsym value: 0.13
Reflection
*PLUS
Rmerge(I) obs: 0.13

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.244 --THIN SHELLS
Rwork0.204 ---
obs0.204 5551 99.5 %-
all-5551 --
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1272 0 5 5 1282
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.452
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.76
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.143
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 20 Å / σ(F): 0 / Rfactor obs: 0.205
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.76
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.143

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