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- PDB-1cgf: CRYSTAL STRUCTURES OF RECOMBINANT 19-KDA HUMAN FIBROBLAST COLLAGE... -

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Basic information

Entry
Database: PDB / ID: 1cgf
TitleCRYSTAL STRUCTURES OF RECOMBINANT 19-KDA HUMAN FIBROBLAST COLLAGENASE COMPLEXED TO ITSELF
ComponentsFIBROBLAST COLLAGENASE
KeywordsHYDROLASE (METALLOPROTEASE)
Function / homology
Function and homology information


interstitial collagenase / cellular response to UV-A / protein metabolic process / Basigin interactions / Activation of Matrix Metalloproteinases / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / extracellular matrix / Degradation of the extracellular matrix ...interstitial collagenase / cellular response to UV-A / protein metabolic process / Basigin interactions / Activation of Matrix Metalloproteinases / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / extracellular matrix / Degradation of the extracellular matrix / extracellular matrix organization / positive regulation of protein-containing complex assembly / metalloendopeptidase activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / peptidase activity / Interleukin-4 and Interleukin-13 signaling / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / zinc ion binding / extracellular region
Similarity search - Function
Peptidoglycan binding-like / 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 ...Peptidoglycan binding-like / 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 / Neutral zinc metallopeptidases, zinc-binding region signature. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Interstitial collagenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsLovejoy, B. / Hassell, A.M. / Luther, M.A. / Weigl, D. / Jordan, S.R.
Citation
Journal: Biochemistry / Year: 1994
Title: Crystal structures of recombinant 19-kDa human fibroblast collagenase complexed to itself.
Authors: Lovejoy, B. / Hassell, A.M. / Luther, M.A. / Weigl, D. / Jordan, S.R.
#1: Journal: Science / Year: 1994
Title: Structure of the Catalytic Domain of Fibroblast Collagenase Complexed with an Inhibitor
Authors: Lovejoy, B. / Cleasby, A. / Hassell, A.M. / Longley, K. / Luther, M.A. / Weigl, D. / Mcgeehan, G. / Mcelroy, A.B. / Drewry, D. / Lambert, M.H. / Jordan, S.R.
History
DepositionFeb 3, 1994Processing site: BNL
Revision 1.0Mar 31, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.process_site / _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

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Assembly

Deposited unit
A: FIBROBLAST COLLAGENASE
B: FIBROBLAST COLLAGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,82012
Polymers36,3182
Non-polymers50210
Water3,261181
1
A: FIBROBLAST COLLAGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4106
Polymers18,1591
Non-polymers2515
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: FIBROBLAST COLLAGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4106
Polymers18,1591
Non-polymers2515
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.000, 50.500, 48.000
Angle α, β, γ (deg.)90.00, 100.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein FIBROBLAST COLLAGENASE


Mass: 18158.775 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDNA / References: UniProt: P03956, interstitial collagenase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE WAS DERIVED FROM THE CDNA SEQUENCE OF G. I. GOLDBERG, ET AL., J. BIOL. CHEM. 261: 6600- ...THE SEQUENCE WAS DERIVED FROM THE CDNA SEQUENCE OF G. I. GOLDBERG, ET AL., J. BIOL. CHEM. 261: 6600-660 (1986), AND DESCRIBED IN THE JRNL REFERENCE ABOVE. N-TERMINAL MASS SPECTROMETRY ANALYSIS OF DISSOLVED CRYSTALS CONFIRMED THAT LEU 102 REPRESENTS THE AMINO TERMINUS.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.26 %
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / PH range low: 9 / PH range high: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12 Msodium formate11
21 mMcalcium chloride11
30.05 Mzinc chloride11
40.1 MTris-HCl11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.1 Å / Num. obs: 17088 / % possible obs: 86.7 % / Rmerge(I) obs: 0.062

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.1→7 Å / σ(F): 1 /
RfactorNum. reflection
Rwork0.197 -
obs0.197 17088
Refinement stepCycle: LAST / Resolution: 2.1→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3094 0 10 543 3647
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg2.06
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.06

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