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- PDB-4jij: Crystal structure of an inactive mutant of MMP-9 catalytic domain... -

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Basic information

Entry
Database: PDB / ID: 4jij
TitleCrystal structure of an inactive mutant of MMP-9 catalytic domain in complex with a fluorogenic synthetic peptidic substrate
Components
  • Matrix metalloproteinase-9
  • fluorogenic peptidic substrate (8MC)PLG(PHI)(DNW)AR(NH2)
KeywordsHYDROLASE/substrate / HYDROLASE substrate complex / Zincin-like / Gelatinase / Collagenase / Catalytic Domain / HYDROLASE-substrate complex
Function / homology
Function and homology information


gelatinase B / negative regulation of epithelial cell differentiation involved in kidney development / : / : / cellular response to UV-A / regulation of neuroinflammatory response / positive regulation of keratinocyte migration / Assembly of collagen fibrils and other multimeric structures / positive regulation of DNA binding / positive regulation of epidermal growth factor receptor signaling pathway ...gelatinase B / negative regulation of epithelial cell differentiation involved in kidney development / : / : / cellular response to UV-A / regulation of neuroinflammatory response / positive regulation of keratinocyte migration / Assembly of collagen fibrils and other multimeric structures / positive regulation of DNA binding / positive regulation of epidermal growth factor receptor signaling pathway / Activation of Matrix Metalloproteinases / negative regulation of intrinsic apoptotic signaling pathway / positive regulation of release of cytochrome c from mitochondria / endodermal cell differentiation / response to amyloid-beta / Collagen degradation / collagen catabolic process / macrophage differentiation / extracellular matrix disassembly / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / collagen binding / positive regulation of vascular associated smooth muscle cell proliferation / Degradation of the extracellular matrix / extracellular matrix organization / embryo implantation / skeletal system development / Signaling by SCF-KIT / metalloendopeptidase activity / positive regulation of protein phosphorylation / metallopeptidase activity / tertiary granule lumen / cell migration / peptidase activity / : / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / endopeptidase activity / ficolin-1-rich granule lumen / Extra-nuclear estrogen signaling / positive regulation of apoptotic process / serine-type endopeptidase activity / apoptotic process / Neutrophil degranulation / negative regulation of apoptotic process / proteolysis / extracellular space / extracellular exosome / extracellular region / zinc ion binding / identical protein binding
Similarity search - Function
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 ...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. / 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. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
AZIDE ION / DI(HYDROXYETHYL)ETHER / S-1,2-PROPANEDIOL / STRONTIUM ION / Matrix metalloproteinase-9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.698 Å
AuthorsStura, E.A. / Vera, L. / Cassar-Lajeunesse, E. / Tranchant, I. / Amoura, M. / Dive, V.
CitationJournal: Chem.Biol. / Year: 2014
Title: Halogen Bonding Controls Selectivity of FRET Substrate Probes for MMP-9.
Authors: Tranchant, I. / Vera, L. / Czarny, B. / Amoura, M. / Cassar, E. / Beau, F. / Stura, E.A. / Dive, V.
History
DepositionMar 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2014Group: Database references
Revision 1.2Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_asym_id / _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_asym_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_asym_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
P: fluorogenic peptidic substrate (8MC)PLG(PHI)(DNW)AR(NH2)
A: Matrix metalloproteinase-9
Q: fluorogenic peptidic substrate (8MC)PLG(PHI)(DNW)AR(NH2)
B: Matrix metalloproteinase-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,53425
Polymers39,0674
Non-polymers1,46721
Water7,386410
1
P: fluorogenic peptidic substrate (8MC)PLG(PHI)(DNW)AR(NH2)
A: Matrix metalloproteinase-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,32013
Polymers19,5332
Non-polymers78711
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-124 kcal/mol
Surface area8700 Å2
MethodPISA
2
Q: fluorogenic peptidic substrate (8MC)PLG(PHI)(DNW)AR(NH2)
B: Matrix metalloproteinase-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,21412
Polymers19,5332
Non-polymers68010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-124 kcal/mol
Surface area8670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.200, 57.400, 172.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein/peptide / Protein , 2 types, 4 molecules PQAB

#1: Protein/peptide fluorogenic peptidic substrate (8MC)PLG(PHI)(DNW)AR(NH2)


Mass: 1253.063 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: fluorogenic synthetic L-peptide substrate with MMP-9 specificity.
#2: Protein Matrix metalloproteinase-9 / MMP-9 / 92 kDa gelatinase / 92 kDa type IV collagenase / Gelatinase B / GELB / 67 kDa matrix ...MMP-9 / 92 kDa gelatinase / 92 kDa type IV collagenase / Gelatinase B / GELB / 67 kDa matrix metalloproteinase-9 / 82 kDa matrix metalloproteinase-9


Mass: 18280.283 Da / Num. of mol.: 2 / Mutation: E402A
Source method: isolated from a genetically manipulated source
Details: construct: 110 216 and 392 444 Mutagenesis: Glu402Ala Structure: renumbered omi tting missing domain.
Source: (gene. exp.) Homo sapiens (human) / Gene: CLG4B, MMP9 / Plasmid: pET-14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3 star) / References: UniProt: P14780, gelatinase B

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Non-polymers , 9 types, 431 molecules

#3: Chemical ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: N3
#4: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-SR / STRONTIUM ION


Mass: 87.620 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Sr
#7: Chemical ChemComp-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O2
#8: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#10: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 410 / 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: 2.22 Å3/Da / Density % sol: 44.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Protein: 6 microL hMMP9(E402A) at 181 micro-M 0.12 M acetohydroxamic acid and 0.3 microL IT34-I at 6.9 mill-M. Reservoir: 10% PEG 20K, 0.1 M MMT (L-malic acid, MES, Tris) 75% acid/25% basic, ...Details: Protein: 6 microL hMMP9(E402A) at 181 micro-M 0.12 M acetohydroxamic acid and 0.3 microL IT34-I at 6.9 mill-M. Reservoir: 10% PEG 20K, 0.1 M MMT (L-malic acid, MES, Tris) 75% acid/25% basic, 0.8 M NaCl, 0.02 SrCl2, 0.01% azide. Cryoprotectant: CryoProtX CM2, 0.8 M Li formate, 0.1 M (MMT 75% acid/25% basic), 9% PEG 10K, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 17, 2012 / Details: mirrors
RadiationMonochromator: Channel cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.698→50 Å / Num. all: 38532 / Num. obs: 38427 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.97 % / Biso Wilson estimate: 23.385 Å2 / Rmerge(I) obs: 0.174 / Rsym value: 0.168 / Net I/σ(I): 9.91
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
1.7-1.88.921.0522.0661441.08398.5
1.8-1.929.140.6813.3957480.686100
1.92-2.089.090.4295.353620.446100
2.08-2.289.380.2857.8949910.294100
2.28-2.548.970.2269.7544890.223100
2.54-2.949.250.16513.2240190.154100
2.94-3.598.670.10519.4434400.092100
3.59-5.078.30.07427.4227120.06499.8
5.07-507.830.07326.616210.06399.7

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Processing

Software
NameVersionClassification
DNAdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4H3X

4h3x


Resolution: 1.698→40.568 Å / SU ML: 0.14 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2.01 / σ(I): -3 / Phase error: 16.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1954 1922 5 %RANDOM
Rwork0.1597 ---
all0.1602 38427 --
obs0.1615 38419 99.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.68 Å2
Refinement stepCycle: LAST / Resolution: 1.698→40.568 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2764 0 61 410 3235
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063047
X-RAY DIFFRACTIONf_angle_d1.0844155
X-RAY DIFFRACTIONf_dihedral_angle_d16.9041043
X-RAY DIFFRACTIONf_chiral_restr0.08399
X-RAY DIFFRACTIONf_plane_restr0.006554
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.6977-1.74020.27931300.23622474260497
1.7402-1.78720.2381370.203125852722100
1.7872-1.83980.22471330.187725452678100
1.8398-1.89920.20391380.171926142752100
1.8992-1.96710.19661340.157925442678100
1.9671-2.04580.20361360.156425752711100
2.0458-2.13890.18061380.143626282766100
2.1389-2.25170.16061350.147825612696100
2.2517-2.39270.18811370.151826092746100
2.3927-2.57750.18861360.156725872723100
2.5775-2.83680.2251390.16226352774100
2.8368-3.24710.23471390.164126362775100
3.2471-4.09040.16481410.138526792820100
4.0904-40.57940.18021490.161828252974100

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