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- PDB-1jj9: Crystal Structure of MMP8-Barbiturate Complex Reveals Mechanism f... -

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Basic information

Entry
Database: PDB / ID: 1jj9
TitleCrystal Structure of MMP8-Barbiturate Complex Reveals Mechanism for Collagen Substrate Recognition
ComponentsMatrix Metalloproteinase 8
KeywordsHYDROLASE / MMP-8 / substrate recognition / cis-peptide bond / conformational transition
Function / homology
Function and homology information


neutrophil collagenase / tumor necrosis factor binding / positive regulation of microglial cell activation / positive regulation of neuroinflammatory response / positive regulation of tumor necrosis factor-mediated signaling pathway / Activation of Matrix Metalloproteinases / endodermal cell differentiation / Collagen degradation / collagen catabolic process / extracellular matrix disassembly ...neutrophil collagenase / tumor necrosis factor binding / positive regulation of microglial cell activation / positive regulation of neuroinflammatory response / positive regulation of tumor necrosis factor-mediated signaling pathway / Activation of Matrix Metalloproteinases / endodermal cell differentiation / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / Degradation of the extracellular matrix / extracellular matrix organization / metalloendopeptidase activity / specific granule lumen / positive regulation of tumor necrosis factor production / tertiary granule lumen / peptidase activity / cellular response to lipopolysaccharide / collagen-containing extracellular matrix / endopeptidase activity / serine-type endopeptidase activity / Neutrophil degranulation / 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
Chem-BBT / Neutrophil collagenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBrandstetter, H. / Grams, F. / Glitz, D. / Lang, A. / Huber, R. / Bode, W. / Krell, H.-W. / Engh, R.A.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: The 1.8-A crystal structure of a matrix metalloproteinase 8-barbiturate inhibitor complex reveals a previously unobserved mechanism for collagenase substrate recognition.
Authors: Brandstetter, H. / Grams, F. / Glitz, D. / Lang, A. / Huber, R. / Bode, W. / Krell, H.W. / Engh, R.A.
History
DepositionJul 4, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 1, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory / Refinement description
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / software
Item: _software.name
Revision 1.4Mar 13, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / 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

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Assembly

Deposited unit
A: Matrix Metalloproteinase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6546
Polymers18,1121
Non-polymers5425
Water3,333185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.02, 69.23, 88.47
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Matrix Metalloproteinase 8 / NEUTROPHIL COLLAGENASE


Mass: 18111.744 Da / Num. of mol.: 1 / Fragment: catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P22894, neutrophil collagenase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-BBT / 2-HYDROXY-5-[4-(2-HYDROXY-ETHYL)-PIPERIDIN-1-YL]-5-PHENYL-1H-PYRIMIDINE-4,6-DIONE


Mass: 331.366 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N3O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6
Details: PEG6000, 10mM CaCl2, 100mM NaCl, Cacodylate pH6.0, VAPOR DIFFUSION, temperature 291K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / PH range low: 6.5 / PH range high: 5.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
13.6 mg/mlprotein1drop
240 mMcacodylate1drop
34 mM1dropCaCl2
440 mM1dropNaCl
54 %PEG60001drop
60.5-0.6 Mphosphate1reservoir

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Data collection

DiffractionMean temperature: 275 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: XENTRONICS / Detector: AREA DETECTOR / Date: Jun 27, 1996 / Details: monochromator
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 16907 / Num. obs: 14371 / % possible obs: 85 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3
Reflection shellResolution: 1.8→20 Å / % possible all: 85
Reflection
*PLUS
% possible obs: 85 % / Rmerge(I) obs: 0.093
Reflection shell
*PLUS
Rmerge(I) obs: 0.41

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1refinement
X-GENdata reduction
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→8 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.296 521 4.8 %random
Rwork0.211 ---
all-11862 --
obs-10862 --
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1249 0 28 185 1462
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_angle_d1.6
LS refinement shellResolution: 2→8 Å
RfactorNum. reflection
Rfree0.296 521
Rwork0.211 -
obs-11713
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 4.8 % / Rfactor obs: 0.211
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.7
LS refinement shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 8 Å / Rfactor Rfree: 0.296 / Rfactor Rwork: 0.211

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