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- PDB-4h2e: Crystal structure of an MMP twin inhibitor complexing two MMP-9 c... -

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Basic information

Entry
Database: PDB / ID: 4h2e
TitleCrystal structure of an MMP twin inhibitor complexing two MMP-9 catalytic domains
ComponentsMatrix metalloproteinase-9
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE/TWIN INHIBITOR / Zincin-like / Gelatinase / Collagenase (Catalytic Domain) / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


gelatinase B / negative regulation of epithelial cell differentiation involved in kidney development / negative regulation of cation channel activity / : / cellular response to UV-A / regulation of neuroinflammatory response / positive regulation of keratinocyte migration / positive regulation of epidermal growth factor receptor signaling pathway / Assembly of collagen fibrils and other multimeric structures / positive regulation of DNA binding ...gelatinase B / negative regulation of epithelial cell differentiation involved in kidney development / negative regulation of cation channel activity / : / cellular response to UV-A / regulation of neuroinflammatory response / positive regulation of keratinocyte migration / positive regulation of epidermal growth factor receptor signaling pathway / Assembly of collagen fibrils and other multimeric structures / positive regulation of DNA binding / positive regulation of release of cytochrome c from mitochondria / Activation of Matrix Metalloproteinases / endodermal cell differentiation / response to amyloid-beta / Collagen degradation / macrophage differentiation / collagen catabolic process / extracellular matrix disassembly / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / negative regulation of intrinsic apoptotic signaling pathway / positive regulation of vascular associated smooth muscle cell proliferation / collagen binding / cellular response to cadmium ion / embryo implantation / Degradation of the extracellular matrix / extracellular matrix organization / positive regulation of receptor binding / skeletal system development / Signaling by SCF-KIT / metalloendopeptidase activity / cellular response to reactive oxygen species / metallopeptidase activity / cell migration / tertiary granule lumen / peptidase activity / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / collagen-containing extracellular matrix / endopeptidase activity / ficolin-1-rich granule lumen / Extra-nuclear estrogen signaling / positive regulation of apoptotic process / positive regulation of protein phosphorylation / serine-type endopeptidase activity / Neutrophil degranulation / negative regulation of apoptotic process / apoptotic process / proteolysis / extracellular space / extracellular exosome / zinc ion binding / extracellular region / 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
Chem-0Y3 / ACETATE ION / DI(HYDROXYETHYL)ETHER / Matrix metalloproteinase-9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLREP / Resolution: 2.902 Å
AuthorsStura, E.A. / Vera, L. / Cassar-Lajeunesse, E. / Nuti, E. / Catalani, M.P. / Dive, V. / Rossello, A.
CitationJournal: J.Struct.Biol. / Year: 2013
Title: Crystallization of bi-functional ligand protein complexes.
Authors: Antoni, C. / Vera, L. / Devel, L. / Catalani, M.P. / Czarny, B. / Cassar-Lajeunesse, E. / Nuti, E. / Rossello, A. / Dive, V. / Stura, E.A.
History
DepositionSep 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1May 1, 2013Group: Database references
Revision 1.2Oct 8, 2014Group: Structure summary
Revision 1.3Aug 12, 2015Group: Database references
Revision 1.4May 31, 2017Group: Structure summary
Revision 1.5Sep 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_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.pdbx_dist_value / _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_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

Downloads & links

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Assembly

Deposited unit
A: Matrix metalloproteinase-9
B: Matrix metalloproteinase-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,93528
Polymers36,6772
Non-polymers3,25826
Water2,666148
1
A: Matrix metalloproteinase-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,68916
Polymers18,3381
Non-polymers1,35115
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Matrix metalloproteinase-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,24512
Polymers18,3381
Non-polymers1,90711
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.180, 97.400, 45.690
Angle α, β, γ (deg.)90.00, 111.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Matrix metalloproteinase-9 / MMP-9 / 92 kDa gelatinase / 92 kDa type IV collagenase / Gelatinase B


Mass: 18338.318 Da / Num. of mol.: 2 / Fragment: unp residues 110-214 and 391-444 / Mutation: E402Q,E402Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MMP9, CLG4B / 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 , 7 types, 174 molecules

#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.: 5 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#7: Chemical ChemComp-0Y3 / N,N'-bis(4-{[(3R)-3-[(biphenyl-4-ylsulfonyl)(propan-2-yloxy)amino]-4-(hydroxyamino)-4-oxobutyl]amino}-4-oxobutyl)benzene-1,3-dicarboxamide


Mass: 1115.277 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C54H66N8O14S2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.26 Å3/Da / Density % sol: 45.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: protein: hMMP-9-WT at 2 mg/mL with 120 milli-M acetohydroxamic acid. Reservoir: 40% monomethyl PEG 5,000, 0.1 M glycine. Cryoprotectant: 35% MPEG 5K, 15% PEG 400, 15% AAB buffer at pH 8.0 , ...Details: protein: hMMP-9-WT at 2 mg/mL with 120 milli-M acetohydroxamic acid. Reservoir: 40% monomethyl PEG 5,000, 0.1 M glycine. Cryoprotectant: 35% MPEG 5K, 15% PEG 400, 15% AAB buffer at pH 8.0 , 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: 0.98011 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 20, 2010 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 7301 / Num. obs: 7158 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.15 % / Biso Wilson estimate: 26.65 Å2 / Rmerge(I) obs: 0.195 / Rsym value: 0.17 / Net I/σ(I): 7.01
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
2.9-3.084.120.532.911890.46396.5
3.08-3.294.220.3354.410930.29398.2
3.29-3.554.230.2745.5210120.2498.4
3.55-3.894.190.1867.369470.16298.6
3.89-4.344.160.1468.788510.12798.7
4.34-5.014.10.13610.047700.11897.8
5.01-6.124.10.1498.776330.1399.1
6.12-8.584.010.11410.065100.09997.8
8.58-5040.07314.842960.06397.6

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Processing

Software
NameVersionClassification
DNAdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.8_1069)/REFMACrefinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLREP
Starting model: 4H1Q

4h1q


Resolution: 2.902→38.85 Å / SU ML: 0.45 / Isotropic thermal model: grouped/Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): -3 / Phase error: 30.8 / Stereochemistry target values: ML / Details: Both REFMAC and PHENIX used
RfactorNum. reflection% reflectionSelection details
Rfree0.3114 357 5.01 %RANDOM
Rwork0.2771 ---
obs0.279 7128 98.03 %-
all-7158 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.01 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å20 Å21.07 Å2
2---1.1 Å20 Å2
3---1.17 Å2
Refinement stepCycle: LAST / Resolution: 2.902→38.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2608 0 199 148 2955
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112910
X-RAY DIFFRACTIONf_angle_d1.4583928
X-RAY DIFFRACTIONf_dihedral_angle_d26.6621056
X-RAY DIFFRACTIONf_chiral_restr0.084368
X-RAY DIFFRACTIONf_plane_restr0.008519
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.9025-3.32230.30091180.26652238223897
3.3223-4.18490.32181190.26212260226099
4.1849-38.85340.30831200.29792273227398

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