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- PDB-830c: COLLAGENASE-3 (MMP-13) COMPLEXED TO A SULPHONE-BASED HYDROXAMIC ACID -

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Basic information

Entry
Database: PDB / ID: 830c
TitleCOLLAGENASE-3 (MMP-13) COMPLEXED TO A SULPHONE-BASED HYDROXAMIC ACID
ComponentsMMP-13Matrix metallopeptidase 13
KeywordsMATRIX METALLOPROTEASE
Function / homology
Function and homology information


growth plate cartilage development / RUNX2 regulates genes involved in cell migration / endochondral ossification / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / bone morphogenesis / Assembly of collagen fibrils and other multimeric structures / bone mineralization / Activation of Matrix Metalloproteinases / response to amyloid-beta / Collagen degradation ...growth plate cartilage development / RUNX2 regulates genes involved in cell migration / endochondral ossification / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / bone morphogenesis / Assembly of collagen fibrils and other multimeric structures / bone mineralization / Activation of Matrix Metalloproteinases / response to amyloid-beta / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / collagen binding / Degradation of the extracellular matrix / extracellular matrix organization / extracellular matrix / metalloendopeptidase activity / endopeptidase activity / serine-type endopeptidase activity / calcium ion binding / 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-RS1 / Collagenase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLovejoy, B. / Welch, A. / Carr, S. / Luong, C. / Broka, C. / Hendricks, R.T. / Campbell, J. / Walker, K. / Martin, R. / Van Wart, H. / Browner, M.F.
CitationJournal: Nat.Struct.Biol. / Year: 1999
Title: Crystal structures of MMP-1 and -13 reveal the structural basis for selectivity of collagenase inhibitors.
Authors: Lovejoy, B. / Welch, A.R. / Carr, S. / Luong, C. / Broka, C. / Hendricks, R.T. / Campbell, J.A. / Walker, K.A. / Martin, R. / Van Wart, H. / Browner, M.F.
History
DepositionAug 6, 1998Processing site: BNL
Revision 1.0Aug 6, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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.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
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MMP-13
B: MMP-13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,01210
Polymers37,8182
Non-polymers1,1948
Water6,612367
1
A: MMP-13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5065
Polymers18,9091
Non-polymers5974
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MMP-13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5065
Polymers18,9091
Non-polymers5974
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)136.072, 36.098, 96.368
Angle α, β, γ (deg.)90.00, 131.06, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein MMP-13 / Matrix metallopeptidase 13 / MMP-13


Mass: 18909.076 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN
Source method: isolated from a genetically manipulated source
Details: CATALYTIC DOMAIN IS COMPLEXED WITH A DIPHENYL-ETHER, SULPHONE INHIBITOR
Source: (gene. exp.) Homo sapiens (human)
Description: HUMAN CDNA CONSTRUCT. CDNA CONSTRUCT OF PROCOLLAGENASE-3
Production host: Escherichia coli (E. coli)
References: UniProt: P45452, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#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.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-RS1 / 4-[4-(4-CHLORO-PHENOXY)-BENZENESULFONYLMETHYL]-TETRAHYDRO-PYRAN-4-CARBOXYLIC ACID HYDROXYAMIDE


Mass: 425.883 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H20ClNO6S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 367 / 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: 2.36 Å3/Da / Density % sol: 47.84 %
Crystal growpH: 8 / Details: pH 8.0
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
19-12 mg/mlprotein1drop
220 mMTris1drop
35 mM1dropCaCl2
450 mM1dropNaCl
50.3 mMinhibitor1drop
610-14 %PEG40001reservoircan be replaced by PEG8000
71.0-1.5 Mammonium formate1reservoir
8100 mMTris1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1
DetectorType: ADSC / Detector: CCD / Date: Dec 1, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. obs: 43128 / % possible obs: 91 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.087

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CGF

1cgf


Resolution: 1.6→7 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
Details: INHIBITOR REFINED USING PARAMETERS DERIVED FROM QUANTA
RfactorNum. reflection% reflectionSelection details
Rfree0.266 4387 9.3 %RANDOM
Rwork0.208 ---
obs0.208 42846 91 %-
Displacement parametersBiso mean: 14.79 Å2
Refinement stepCycle: LAST / Resolution: 1.6→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2636 0 56 367 3059
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg2.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.13
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.24
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
LS refinement shellResolution: 1.6→1.67 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3567 320 9.3 %
Rwork0.3347 2923 -
obs--56.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.13
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.24

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