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- PDB-1l6j: Crystal structure of human matrix metalloproteinase MMP9 (gelatin... -

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Basic information

Entry
Database: PDB / ID: 1l6j
TitleCrystal structure of human matrix metalloproteinase MMP9 (gelatinase B).
ComponentsMatrix metalloproteinase-9
KeywordsHYDROLASE / Twisted beta sheet flanked by helices
Function / homology
Function and homology information


gelatinase B / negative regulation of epithelial cell differentiation involved in kidney development / negative regulation of cation channel activity / negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / cellular response to UV-A / positive regulation of keratinocyte migration / regulation of neuroinflammatory response / positive regulation of epidermal growth factor receptor signaling pathway / Assembly of collagen fibrils and other multimeric structures / Activation of Matrix Metalloproteinases ...gelatinase B / negative regulation of epithelial cell differentiation involved in kidney development / negative regulation of cation channel activity / negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / cellular response to UV-A / positive regulation of keratinocyte migration / regulation of neuroinflammatory response / positive regulation of epidermal growth factor receptor signaling pathway / Assembly of collagen fibrils and other multimeric structures / Activation of Matrix Metalloproteinases / endodermal cell differentiation / positive regulation of release of cytochrome c from mitochondria / response to amyloid-beta / macrophage differentiation / Collagen degradation / collagen catabolic process / EPH-ephrin mediated repulsion of cells / extracellular matrix disassembly / ephrin receptor signaling pathway / positive regulation of DNA binding / 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 protein phosphorylation / positive regulation of apoptotic process / serine-type endopeptidase activity / apoptotic process / Neutrophil degranulation / negative regulation of apoptotic process / proteolysis / extracellular space / zinc ion binding / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
Fibronectin, type II, collagen-binding / Muramoyl-pentapeptide Carboxypeptidase; domain 1 / PGBD-like superfamily/PGBD / Seminal Fluid Protein PDC-109 (Domain B) / 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 ...Fibronectin, type II, collagen-binding / Muramoyl-pentapeptide Carboxypeptidase; domain 1 / PGBD-like superfamily/PGBD / Seminal Fluid Protein PDC-109 (Domain B) / 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. / 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 / Kringle-like fold / Neutral zinc metallopeptidases, zinc-binding region signature. / Ribbon / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Matrix metalloproteinase-9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsElkins, P.A. / Ho, Y.S. / Smith, W.W. / Janson, C.A. / D'Alessio, K.J. / McQueney, M.S. / Cummings, M.D. / Romanic, A.M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Structure of the C-terminally truncated human ProMMP9, a gelatin-binding matrix metalloproteinase.
Authors: Elkins, P.A. / Ho, Y.S. / Smith, W.W. / Janson, C.A. / D'Alessio, K.J. / McQueney, M.S. / Cummings, M.D. / Romanic, A.M.
History
DepositionMar 11, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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_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-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5966
Polymers47,3441
Non-polymers2515
Water3,441191
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.685, 123.685, 89.937
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Matrix metalloproteinase-9 / MMP9 / Gelatinase B / GELB


Mass: 47344.457 Da / Num. of mol.: 1 / Fragment: pro-form with C-terminal domain truncated
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BLR (DE3) / References: UniProt: P14780, gelatinase B
#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.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 4.19 Å3/Da / Density % sol: 70.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: sodium chloride, Tris, HEPES, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
112.8 mg/mlprotein1drop
220 mMTris1droppH8.2
3100 mM1dropNaCl
44.3 M1reservoirNaCl
50.1 MHEPES1reservoirpH7.0

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.271632, 1.209997, 1.272917
DetectorType: BRANDEIS / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.2716321
21.2099971
31.2729171
ReflectionResolution: 2.5→20 Å / Num. obs: 34009 / % possible obs: 89.1 % / Observed criterion σ(F): -3 / Rmerge(I) obs: 0.077 / Net I/σ(I): 11.5
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.194 / Mean I/σ(I) obs: 2.4 / % possible all: 73.8
Reflection
*PLUS
Num. obs: 47453
Reflection shell
*PLUS
Highest resolution: 2.5 Å / % possible obs: 73.8 % / Num. unique obs: 3904

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: MAD
Starting model: PDB ENTRY 1CK7

1ck7


Resolution: 2.5→19.97 Å / Isotropic thermal model: isotropic / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Structure factor analysis for this report was made by SFCHECK V 5.3.4 using anisotropic scaling and the Babinet bulk solvent correction. The correlation between the experimental map and the ...Details: Structure factor analysis for this report was made by SFCHECK V 5.3.4 using anisotropic scaling and the Babinet bulk solvent correction. The correlation between the experimental map and the model was computed using CCP4/SFALL, CCP4/FFT and CCP4/OVERLAPMAP. The difference between the experimental phases and the model phases was computed using CCP4/SFALL and CCP4/PHISTATS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1265 -RANDOM
Rwork0.187 ---
all-24477 --
obs-24477 89.1 %-
Solvent computationBsol: 250.028 Å2 / ksol: 0.763 e/Å3
Displacement parametersBiso mean: 37 Å2
Refine analyzeLuzzati coordinate error obs: 0.287 Å / Luzzati d res low obs: 5 Å
Refinement stepCycle: LAST / Resolution: 2.5→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3180 0 5 191 3376
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it0.0130.011
X-RAY DIFFRACTIONc_mcangle_it1.842.03
LS refinement shellResolution: 2.5→2.53 Å
RfactorNum. reflection
Rfree0.315 39
Rwork0.272 20219
obs-783
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.223 / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0120.011
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.72.03

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