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- PDB-1hfc: 1.56 ANGSTROM STRUCTURE OF MATURE TRUNCATED HUMAN FIBROBLAST COLL... -

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Basic information

Entry
Database: PDB / ID: 1hfc
Title1.56 ANGSTROM STRUCTURE OF MATURE TRUNCATED HUMAN FIBROBLAST COLLAGENASE
ComponentsFIBROBLAST COLLAGENASE
KeywordsMETALLOPROTEASE
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 / Degradation of the extracellular matrix / extracellular matrix organization ...interstitial collagenase / cellular response to UV-A / protein metabolic process / Basigin interactions / Activation of Matrix Metalloproteinases / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / Degradation of the extracellular matrix / extracellular matrix organization / extracellular matrix / 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
METHYLAMINO-PHENYLALANYL-LEUCYL-HYDROXAMIC ACID / Interstitial collagenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.5 Å
AuthorsSpurlino, J.C. / Smith, D.L.
Citation
#1: Journal: Nat.Struct.Biol. / Year: 1994
Title: Structure of Human Neutrophil Collagenase Reveals Large S1' Specificity Pocket
Authors: Stams, T. / Spurlino, J.C. / Smith, D.L. / Wahl, R.C. / Ho, T.F. / Qoronfleh, M.W. / Banks, T.M. / Rubin, B.
History
DepositionSep 13, 1994Processing site: BNL
Revision 1.0Jan 26, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Jul 17, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.5Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.6Feb 7, 2024Group: 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
Remark 700SHEET S1 AS PRESENTED ON SHEET RECORDS BELOW IS A FIVE-STRANDED SHEET. THE HET GROUP HAP IS LOCATED ...SHEET S1 AS PRESENTED ON SHEET RECORDS BELOW IS A FIVE-STRANDED SHEET. THE HET GROUP HAP IS LOCATED IN SUCH A POSITION THAT IT COULD BE CONSIDERED THE SIXTH STRAND OF THIS SHEET SHEET AND PRO 238 - PHE 242 COULD BE CONSIDERED THE SEVENTH STRAND OF THIS SHEET.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FIBROBLAST COLLAGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3865
Polymers18,8661
Non-polymers5204
Water1,58588
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.210, 44.570, 36.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: RESIDUES GLU 209 AND TYR 210 FORM A CIS-PEPTIDE BOND.

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Components

#1: Protein FIBROBLAST COLLAGENASE


Mass: 18865.541 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P03956, interstitial collagenase
#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.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-PLH / METHYLAMINO-PHENYLALANYL-LEUCYL-HYDROXAMIC ACID


Mass: 349.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H27N3O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.41 %
Crystal grow
*PLUS
pH: 7.5 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein11
22.5 mMTris-HCl11
35.0 mM11CaCl2
40.4 M11NaCl
53 mM11NaN3
61 mMhydroxamate inhibitor11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.56 Å / Lowest resolution: 2.83 Å / Num. obs: 23912 / % possible obs: 89.7 % / Num. measured all: 64262 / Rmerge(I) obs: 0.0642
Reflection shell
*PLUS
Highest resolution: 1.56 Å / Lowest resolution: 1.66 Å / % possible obs: 73.7 % / Num. unique obs: 3218 / Num. measured obs: 5791 / Rmerge(I) obs: 0.2688

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.5→10 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.174 -
obs0.174 21710
Refinement stepCycle: LAST / Resolution: 1.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1245 0 28 88 1361
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
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_deg2.7
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
Software
*PLUS
Name: X-PLOR/PROLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.56 Å / Rfactor obs: 0.174
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d2.7
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_improper_angle_d
X-RAY DIFFRACTIONp_planar_d0.050.055
X-RAY DIFFRACTIONp_plane_restr0.0150.012
X-RAY DIFFRACTIONp_chiral_restr0.20.221
X-RAY DIFFRACTIONp_mcbond_it2.52.126
X-RAY DIFFRACTIONp_scbond_it44.582
X-RAY DIFFRACTIONp_mcangle_it4.52.906
X-RAY DIFFRACTIONp_scangle_it66.816

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