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- PDB-9csx: matrix metalloproteinase-10 proenzyme -

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Basic information

Entry
Database: PDB / ID: 9csx
Titlematrix metalloproteinase-10 proenzyme
ComponentsStromelysin-2
KeywordsHYDROLASE / proteinase
Function / homology
Function and homology information


stromelysin 2 / Activation of Matrix Metalloproteinases / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / Degradation of the extracellular matrix / extracellular matrix organization / extracellular matrix / metalloendopeptidase activity / serine-type endopeptidase activity ...stromelysin 2 / Activation of Matrix Metalloproteinases / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / Degradation of the extracellular matrix / extracellular matrix organization / extracellular matrix / metalloendopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / zinc ion binding
Similarity search - Function
Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidoglycan binding-like / Peptidase M10A, cysteine switch, zinc binding site / Matrixins cysteine switch. / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin / Putative peptidoglycan binding domain ...Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidoglycan binding-like / Peptidase M10A, cysteine switch, zinc binding site / Matrixins cysteine switch. / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin / Putative peptidoglycan binding domain / Hemopexin repeat profile. / Hemopexin-like repeats. / Peptidase M10A / Peptidase M10A, catalytic domain / Peptidase M10, metallopeptidase / Matrixin / PGBD-like superfamily / Peptidase, metallopeptidase / Zinc-dependent metalloprotease / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
ACETIC ACID / IMIDAZOLE / Stromelysin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsIsiorho, E.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Other government95660-00 01 United States
CitationJournal: To Be Published
Title: Matrix metalloproteinase-10 (MMP-10) proenzyme
Authors: Isiorho, E.A.
History
DepositionJul 24, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Stromelysin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,33912
Polymers30,7181
Non-polymers62011
Water4,558253
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.841, 72.003, 54.495
Angle α, β, γ (deg.)90.000, 130.820, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Stromelysin-2 / SL-2 / Matrix metalloproteinase-10 / MMP-10 / Transin-2


Mass: 30718.451 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MMP10, STMY2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P09238, stromelysin 2

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Non-polymers , 5 types, 264 molecules

#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 1.95 Å3/Da / Density % sol: 37.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M zinc acetate, 0.1 M imidazole, pH 7.5 and 17 % (w/v)PEG 3000, 4.0 % (v/v) acetonitrile

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.669→46.621 Å / Num. obs: 25894 / % possible obs: 94.1 % / Redundancy: 2.6 % / Biso Wilson estimate: 16.08 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.159 / Rpim(I) all: 0.115 / Rrim(I) all: 0.197 / Net I/σ(I): 2.8
Reflection shellResolution: 1.669→1.697 Å / Rmerge(I) obs: 0.986 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 1322 / CC1/2: 0.339 / Rpim(I) all: 0.731

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.67→27.12 Å / SU ML: 0.2033 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.9413
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2126 1247 4.88 %
Rwork0.1888 24283 -
obs0.19 25530 92.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.03 Å2
Refinement stepCycle: LAST / Resolution: 1.67→27.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1834 0 22 253 2109
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00781899
X-RAY DIFFRACTIONf_angle_d0.96782568
X-RAY DIFFRACTIONf_chiral_restr0.0522269
X-RAY DIFFRACTIONf_plane_restr0.0229336
X-RAY DIFFRACTIONf_dihedral_angle_d6.5853247
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.67-1.740.33711160.28872571X-RAY DIFFRACTION89.06
1.74-1.810.34941220.26072723X-RAY DIFFRACTION92.97
1.81-1.910.2431240.2372772X-RAY DIFFRACTION95.39
1.91-2.030.2781170.21982786X-RAY DIFFRACTION94.59
2.03-2.190.22971690.18792710X-RAY DIFFRACTION94.3
2.19-2.410.20531600.17452718X-RAY DIFFRACTION94.76
2.41-2.750.21650.17012699X-RAY DIFFRACTION93.35
2.75-3.470.18961210.17232675X-RAY DIFFRACTION91.25
3.47-27.120.17691530.16442629X-RAY DIFFRACTION89.17

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