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- PDB-1br9: HUMAN TISSUE INHIBITOR OF METALLOPROTEINASE-2 -

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Basic information

Entry
Database: PDB / ID: 1br9
TitleHUMAN TISSUE INHIBITOR OF METALLOPROTEINASE-2
ComponentsMETALLOPROTEINASE-2 INHIBITOR
KeywordsPROTEINASE INHIBITOR
Function / homology
Function and homology information


negative regulation of metallopeptidase activity / negative regulation of membrane protein ectodomain proteolysis / metalloendopeptidase inhibitor activity / TGFBR3 PTM regulation / peptidase inhibitor activity / molecular function inhibitor activity / Activation of Matrix Metalloproteinases / response to hormone / response to cytokine / extracellular matrix ...negative regulation of metallopeptidase activity / negative regulation of membrane protein ectodomain proteolysis / metalloendopeptidase inhibitor activity / TGFBR3 PTM regulation / peptidase inhibitor activity / molecular function inhibitor activity / Activation of Matrix Metalloproteinases / response to hormone / response to cytokine / extracellular matrix / specific granule lumen / tertiary granule lumen / : / protease binding / ficolin-1-rich granule lumen / Neutrophil degranulation / extracellular space / extracellular region / zinc ion binding
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 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Alpha-Beta Complex / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Metalloproteinase inhibitor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsTuuttila, A. / Morgunova, E. / Bergmann, U. / Lindqvist, Y. / Tryggvason, K. / Schneider, G.
CitationJournal: J.Mol.Biol. / Year: 1998
Title: Three-dimensional structure of human tissue inhibitor of metalloproteinases-2 at 2.1 A resolution.
Authors: Tuuttila, A. / Morgunova, E. / Bergmann, U. / Lindqvist, Y. / Maskos, K. / Fernandez-Catalan, C. / Bode, W. / Tryggvason, K. / Schneider, G.
History
DepositionAug 28, 1998Processing site: BNL
Revision 1.0May 4, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: METALLOPROTEINASE-2 INHIBITOR


Theoretical massNumber of molelcules
Total (without water)21,7831
Polymers21,7831
Non-polymers00
Water1,13563
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.050, 52.700, 46.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein METALLOPROTEINASE-2 INHIBITOR / TIMP-2 / TISSUE INHIBITOR OF METALLOPROTEINASE-2


Mass: 21783.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): H5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P16035
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.15 Å3/Da / Density % sol: 38.74 %
Crystal growpH: 8 / Details: pH 8.0
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110-15 mg/mlprotein1drop
20.1 MTris-HCl1reservoir
30.1 M1reservoirNaCl
430 %(w/v)PEG4001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9095
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9095 Å / Relative weight: 1
ReflectionResolution: 2.1→15 Å / Num. obs: 10532 / % possible obs: 98.8 % / Redundancy: 10 % / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 15.4
Reflection shellResolution: 2.1→2.2 Å / Rmerge(I) obs: 0.284 / Mean I/σ(I) obs: 4.6 / Rsym value: 0.284 / % possible all: 98.5
Reflection
*PLUS
Num. measured all: 100589
Reflection shell
*PLUS
% possible obs: 98.5 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: BOVINE TISSUE INHIBITOR, FERNANDEZ-CATALAN ET AL., 1998, EMBO J., IN PRESS

Resolution: 2.1→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Details: INITIAL REFINEMENT WITH X-PLOR, THEN REFMAC
RfactorNum. reflection% reflectionSelection details
Rfree0.271 528 5 %RANDOM
Rwork0.238 ---
obs-10532 98.8 %-
Displacement parametersBiso mean: 34 Å2
Refinement stepCycle: LAST / Resolution: 2.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1419 0 0 63 1482
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0070.02
X-RAY DIFFRACTIONp_angle_d0.024
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.238
Solvent computation
*PLUS
Displacement parameters
*PLUS

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