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- PDB-1ck7: GELATINASE A (FULL-LENGTH) -

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Basic information

Entry
Database: PDB / ID: 1ck7
TitleGELATINASE A (FULL-LENGTH)
ComponentsPROTEIN (GELATINASE A)
KeywordsHYDROLASE / HYDROLASE (METALLOPROTEASE) / FULL-LENGTH / METALLOPROTEINASE / GELATINASE A
Function / homology
Function and homology information


gelatinase A / peripheral nervous system axon regeneration / blood vessel maturation / parturition / luteinization / bone trabecula formation / tissue remodeling / intramembranous ossification / cellular response to UV-A / ovulation from ovarian follicle ...gelatinase A / peripheral nervous system axon regeneration / blood vessel maturation / parturition / luteinization / bone trabecula formation / 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 / Activation of Matrix Metalloproteinases / endodermal cell differentiation / macrophage chemotaxis / response to amyloid-beta / fibronectin binding / Collagen degradation / collagen catabolic process / EPH-ephrin mediated repulsion of cells / extracellular matrix disassembly / ephrin receptor signaling pathway / response to hyperoxia / cellular response to interleukin-1 / response to electrical stimulus / response to mechanical stimulus / response to retinoic acid / ovarian follicle development / positive regulation of vascular associated smooth muscle cell proliferation / embryo implantation / Degradation of the extracellular matrix / sarcomere / extracellular matrix organization / response to activity / cellular response to estradiol stimulus / cellular response to amino acid stimulus / response to nicotine / protein catabolic process / response to hydrogen peroxide / metalloendopeptidase activity / cellular response to reactive oxygen species / response to estrogen / metallopeptidase activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / heart development / angiogenesis / Interleukin-4 and Interleukin-13 signaling / collagen-containing extracellular matrix / 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, collagen-binding / 4 Propeller / Hemopexin / Hemopexin-like domain / Seminal Fluid Protein PDC-109 (Domain B) / 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 II, collagen-binding / 4 Propeller / Hemopexin / Hemopexin-like domain / Seminal Fluid Protein PDC-109 (Domain B) / 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. / Putative peptidoglycan binding domain / 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. / Ribbon / 3-Layer(aba) Sandwich / Mainly Beta / 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
AuthorsMorgunova, E. / Tuuttila, A. / Bergmann, U. / Isupov, M. / Lindqvist, Y. / Schneider, G. / Tryggvason, K.
CitationJournal: Science / Year: 1999
Title: Structure of human pro-matrix metalloproteinase-2: activation mechanism revealed.
Authors: Morgunova, E. / Tuuttila, A. / Bergmann, U. / Isupov, M. / Lindqvist, Y. / Schneider, G. / Tryggvason, K.
History
DepositionApr 28, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Aug 25, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Apr 11, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_beamline
Revision 1.5Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (GELATINASE A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,49710
Polymers70,9951
Non-polymers5029
Water1,874104
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.320, 121.320, 345.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

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Protein , 1 types, 1 molecules A

#1: Protein PROTEIN (GELATINASE A) / MMP-2 / 72KD TYPE IV COLLAGENASE


Mass: 70995.406 Da / Num. of mol.: 1 / Fragment: FULL-LENGTH / Mutation: E404A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PVL1393 / Cell line (production host): HIGH 5 / Gene (production host): CLG4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P08253, gelatinase A

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Non-polymers , 6 types, 113 molecules

#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: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 4.49 Å3/Da / Density % sol: 72 %
Crystal growpH: 7.8 / Details: pH 7.8
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
20.2 Msodium glycine1reservoir
324-25 %mPEG5501reservoir
40.28 M1reservoirLi2SO4
50.01 Mdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM02 / Wavelength: 0.97984
DetectorDetector: CCD / Date: Oct 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97984 Å / Relative weight: 1
ReflectionResolution: 2.8→34 Å / Num. obs: 32057 / % possible obs: 99.7 % / Redundancy: 10.2 % / Biso Wilson estimate: 105 Å2 / Rsym value: 0.117 / Net I/σ(I): 20.9
Reflection shellResolution: 2.8→2.98 Å / Redundancy: 10.5 % / Mean I/σ(I) obs: 2 / Rsym value: 0.403 / % possible all: 95.4
Reflection
*PLUS
Num. measured all: 333608 / Rmerge(I) obs: 0.117
Reflection shell
*PLUS
% possible obs: 99.7 % / Rmerge(I) obs: 0.402

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Processing

Software
NameVersionClassification
XDSdata scaling
SCALAdata scaling
AMoREphasing
REFMACrefinement
XDSdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GEN, PDB ENTRY 1FBL

1gen

1fbl


Resolution: 2.8→34 Å / σ(F): 0
Details: NO ELECTRON DENSITY WAS OBSERVED FOR THE N-TERMINAL RESIDUE ALA 30 AND FOR RESIDUES ASP 450 - THR 460. PRESUMABLY THEY ARE DISORDERED. THESE RESIDUES ARE PART OF A FLEXIBLE LINKAGE BETWEEN ...Details: NO ELECTRON DENSITY WAS OBSERVED FOR THE N-TERMINAL RESIDUE ALA 30 AND FOR RESIDUES ASP 450 - THR 460. PRESUMABLY THEY ARE DISORDERED. THESE RESIDUES ARE PART OF A FLEXIBLE LINKAGE BETWEEN CATALYTIC CORE AND C-TERMINAL HEMOPEXIN PARTS OF MMP-2. RESIDUES 108 - 116 WERE MODELED INTO POOR ELECTRON DENSITY. THE SIDE CHAIN ORIENTATIONS WERE TAKEN FROM THE ROTAMER LIBRARY. THESE RESIDUES ARE IN THE LOOP WHICH CONECTS PROPEPTIDE AND CATALYTIC DOMAIN. THE ELECTRON DENSITY FOR THE SURFACE LOOP 649 - 652 IS WEAK, AND THE INDIVIDUAL B-FACTORS ARE RATHER HIGH.
RfactorNum. reflection% reflectionSelection details
Rfree0.327 1660 5 %RANDOM
Rwork0.286 ---
obs-30959 99.7 %-
Displacement parametersBiso mean: 63.5 Å2
Refinement stepCycle: LAST / Resolution: 2.8→34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4930 0 17 104 5051
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.012
X-RAY DIFFRACTIONp_angle_d0.024
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.7
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 34 Å / % reflection Rfree: 5 % / Rfactor obs: 0.286
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 63.5 Å2

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