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- PDB-3v96: Complex of matrix metalloproteinase-10 catalytic domain (MMP-10cd... -

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Basic information

Entry
Database: PDB / ID: 3v96
TitleComplex of matrix metalloproteinase-10 catalytic domain (MMP-10cd) with tissue inhibitor of metalloproteinases-1 (TIMP-1)
Components
  • Metalloproteinase inhibitor 1
  • Stromelysin-2
KeywordsHYDROLASE INHIBITOR/HYDROLASE / Metzincin / OB-fold / Metalloproteinase / Protease inhibitor / HYDROLASE INHIBITOR-HYDROLASE complex
Function / homology
Function and homology information


stromelysin 2 / regulation of integrin-mediated signaling pathway / negative regulation of metallopeptidase activity / negative regulation of trophoblast cell migration / connective tissue replacement involved in inflammatory response wound healing / negative regulation of membrane protein ectodomain proteolysis / peptidase inhibitor activity / metalloendopeptidase inhibitor activity / cellular response to UV-A / negative regulation of catalytic activity ...stromelysin 2 / regulation of integrin-mediated signaling pathway / negative regulation of metallopeptidase activity / negative regulation of trophoblast cell migration / connective tissue replacement involved in inflammatory response wound healing / negative regulation of membrane protein ectodomain proteolysis / peptidase inhibitor activity / metalloendopeptidase inhibitor activity / cellular response to UV-A / negative regulation of catalytic activity / negative regulation of endopeptidase activity / cartilage development / Activation of Matrix Metalloproteinases / Interleukin-10 signaling / Collagen degradation / basement membrane / collagen catabolic process / extracellular matrix disassembly / Degradation of the extracellular matrix / extracellular matrix organization / extracellular matrix / platelet alpha granule lumen / response to hormone / response to cytokine / cytokine activity / Post-translational protein phosphorylation / growth factor activity / metalloendopeptidase activity / response to peptide hormone / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Platelet degranulation / Interleukin-4 and Interleukin-13 signaling / protease binding / endoplasmic reticulum lumen / serine-type endopeptidase activity / positive regulation of cell population proliferation / negative regulation of apoptotic process / proteolysis / extracellular space / zinc ion binding / extracellular exosome / extracellular region
Similarity search - Function
Tissue inhibitor of metalloproteinase-1. Chain B, domain 1 / Tissue inhibitor of metalloproteinase-1. Chain B, domain 1 / Protease inhibitor I35 (TIMP) / Proteinase inhibitor I35b (TIMP), C-terminal / Tissue inhibitor of metalloproteinase, conserved site / Tissue inhibitor of metalloproteinase / Tissue inhibitors of metalloproteinases signature. / Tissue inhibitor of metalloproteinase family. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #120 / Netrin domain ...Tissue inhibitor of metalloproteinase-1. Chain B, domain 1 / Tissue inhibitor of metalloproteinase-1. Chain B, domain 1 / Protease inhibitor I35 (TIMP) / Proteinase inhibitor I35b (TIMP), C-terminal / Tissue inhibitor of metalloproteinase, conserved site / Tissue inhibitor of metalloproteinase / Tissue inhibitors of metalloproteinases signature. / Tissue inhibitor of metalloproteinase family. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #120 / Netrin domain / NTR domain profile. / Tissue inhibitor of metalloproteinases-like, OB-fold / 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. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Alpha-Beta Complex / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Metalloproteinase inhibitor 1 / Stromelysin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBatra, J. / Soares, A.S. / Radisky, E.S.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Matrix metalloproteinase-10 (MMP-10) interaction with tissue inhibitors of metalloproteinases TIMP-1 and TIMP-2: binding studies and crystal structure.
Authors: Batra, J. / Robinson, J. / Soares, A.S. / Fields, A.P. / Radisky, D.C. / Radisky, E.S.
History
DepositionDec 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Metalloproteinase inhibitor 1
B: Stromelysin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7019
Polymers39,2602
Non-polymers4417
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-94 kcal/mol
Surface area15580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)231.720, 37.682, 39.523
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Metalloproteinase inhibitor 1 / Erythroid-potentiating activity / EPA / Fibroblast collagenase inhibitor / Collagenase inhibitor / ...Erythroid-potentiating activity / EPA / Fibroblast collagenase inhibitor / Collagenase inhibitor / Tissue inhibitor of metalloproteinases 1 / TIMP-1


Mass: 20689.822 Da / Num. of mol.: 1 / Fragment: unp residues 24-207 / Mutation: N30A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLGI, TIMP, TIMP1 / Plasmid: pTT/TIMP1 / Cell line (production host): HEK 293E / Production host: HOMO SAPIENS (human) / References: UniProt: P01033
#2: Protein Stromelysin-2 / SL-2 / Matrix metalloproteinase-10 / MMP-10 / Transin-2


Mass: 18570.561 Da / Num. of mol.: 1 / Fragment: unp residues 99-263
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MMP10, STMY2 / Plasmid: MMP-10cdna / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P09238, stromelysin 2

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Non-polymers , 4 types, 195 molecules

#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 2.2 Å3/Da / Density % sol: 44.03 %
Crystal growTemperature: 298 K / pH: 6.5
Details: 0.1 M sodium dihydrogen phosphate solution, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 26365 / % possible obs: 91.9 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 23.5
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.785 / Mean I/σ(I) obs: 1.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0102refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→35 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.919 / SU B: 13.288 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.266 1326 5 %RANDOM
Rwork0.215 ---
obs0.218 26280 91.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.64 Å2
Baniso -1Baniso -2Baniso -3
1--1.5 Å20 Å20 Å2
2---1.12 Å20 Å2
3---2.62 Å2
Refinement stepCycle: LAST / Resolution: 1.9→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2578 0 15 188 2781
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0222682
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9481.9483650
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7635325
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.70923.44125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.88415426
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5731514
X-RAY DIFFRACTIONr_chiral_restr0.1370.2389
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212055
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9981.51616
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.58322609
X-RAY DIFFRACTIONr_scbond_it2.58231066
X-RAY DIFFRACTIONr_scangle_it3.6644.51038
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.94 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.408 54 -
Rwork0.341 1115 -
obs--57.33 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.849-0.81520.42233.1743-1.45122.62080.1152-0.143-0.24860.04-0.1971-0.2640.01330.40610.08180.2115-0.0346-0.03760.3275-0.00950.0592158.7765.191-5.856
230.236614.71737.830210.049711.437922.2167-1.89192.06043.4614-2.0630.63151.8326-3.4196-0.33811.26040.93320.1055-0.30740.6550.14560.427145.80710.813-22.757
38.18340.01493.05095.0951-1.09042.3825-0.09440.61280.5933-0.5493-0.0406-0.3795-0.12610.58840.1350.3489-0.07260.04440.5179-0.00150.1049161.86613.253-15.362
49.1928-3.6256-1.23977.5496-0.17173.9154-0.05592.8351-0.4035-2.129-1.6552-2.85160.29791.61061.7110.92730.23070.98022.33410.64392.1048168.5974.579-13.629
54.30530.3840.12572.6229-0.90352.32640.05490.0229-0.0269-0.0099-0.1798-0.1433-0.1750.35790.1250.2121-0.0459-0.01650.32420.00030.0196158.2428.662-7.488
629.2786-8.54125.19849.7264-6.32014.4308-0.1032-0.6395-3.41010.54390.42930.965-0.0342-0.1148-0.32610.537-0.0070.12690.49520.24170.8007151.38-8.3138.545
73.7472.6101-1.14466.3883-1.42295.78760.1914-0.8205-0.68031.4147-0.3192-0.2347-1.14550.78540.12770.5977-0.0205-0.0280.79560.26420.261159.3061.1589.732
84.8534-2.84131.41326.1795-0.55171.31980.0409-0.0166-1.15480.23310.16951.3874-0.04590.0945-0.21050.1399-0.02510.03230.12130.02450.4902132.8012.524-5.369
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 23
2X-RAY DIFFRACTION2A24 - 35
3X-RAY DIFFRACTION3A36 - 46
4X-RAY DIFFRACTION4A47 - 58
5X-RAY DIFFRACTION5A59 - 130
6X-RAY DIFFRACTION6A131 - 144
7X-RAY DIFFRACTION7A145 - 178
8X-RAY DIFFRACTION8B105 - 468

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