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- PDB-3ssb: Structure of Insect Metalloproteinase Inhibitor in Complex with T... -

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Basic information

Entry
Database: PDB / ID: 3ssb
TitleStructure of Insect Metalloproteinase Inhibitor in Complex with Thermolysin
Components
  • (Inducible metalloproteinase inhibitor ...) x 2
  • Thermolysin
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Thermolysin fold - Family I8 fold / Metalloprotease Thermolysin inhibitor / Zn Binding / Secreted / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


metalloendopeptidase inhibitor activity / thermolysin / anatomical structure morphogenesis / extracellular matrix organization / wound healing / metalloendopeptidase activity / proteolysis / extracellular space / extracellular region / metal ion binding
Similarity search - Function
Trypsin Inhibitor-like, cysteine rich domain / Serine protease inhibitor-like superfamily / Trypsin Inhibitor like cysteine rich domain / Elastase; domain 1 - #10 / Elastase; domain 1 / PepSY domain / Peptidase propeptide and YPEB domain / Peptidase M4, C-terminal / FTP domain / Peptidase M4 domain ...Trypsin Inhibitor-like, cysteine rich domain / Serine protease inhibitor-like superfamily / Trypsin Inhibitor like cysteine rich domain / Elastase; domain 1 - #10 / Elastase; domain 1 / PepSY domain / Peptidase propeptide and YPEB domain / Peptidase M4, C-terminal / FTP domain / Peptidase M4 domain / Peptidase M4 / Thermolysin metallopeptidase, catalytic domain / Thermolysin metallopeptidase, alpha-helical domain / Fungalysin/Thermolysin Propeptide Motif / Neutral Protease Domain 2 / Neutral Protease; domain 2 / Peptidase M4/M1, CTD superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Thermolysin / Inducible metalloproteinase inhibitor protein
Similarity search - Component
Biological speciesGalleria mellonella (greater wax moth)
Bacillus thermoproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsArolas, J.L. / Botelho, T.O. / Vilcinskas, A. / Gomis-Ruth, F.X.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2011
Title: Structural evidence for standard-mechanism inhibition in metallopeptidases from a complex poised to resynthesize a Peptide bond.
Authors: Arolas, J.L. / Botelho, T.O. / Vilcinskas, A. / Gomis-Ruth, F.X.
History
DepositionJul 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2011Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 13, 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_ref_seq_dif / 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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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: Thermolysin
C: Inducible metalloproteinase inhibitor protein
I: Inducible metalloproteinase inhibitor protein
B: Thermolysin
D: Inducible metalloproteinase inhibitor protein
J: Inducible metalloproteinase inhibitor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,35719
Polymers84,6636
Non-polymers69413
Water10,989610
1
A: Thermolysin
C: Inducible metalloproteinase inhibitor protein
I: Inducible metalloproteinase inhibitor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,72410
Polymers42,3323
Non-polymers3937
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-21 kcal/mol
Surface area15540 Å2
MethodPISA
2
B: Thermolysin
D: Inducible metalloproteinase inhibitor protein
J: Inducible metalloproteinase inhibitor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6329
Polymers42,3323
Non-polymers3016
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-18 kcal/mol
Surface area15480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.640, 78.370, 92.290
Angle α, β, γ (deg.)90.00, 90.08, 90.00
Int Tables number4
Space group name H-MP1211
DetailsAuthor states that inhibitor IMPI alpha maintains its 3D structure (represented by chains C,I and D,J) after being cleaved between residues 56-57. The biological assemnbly is a dimeric complex between a proteinase moiety (chains A or B) and an inhibitor moiety (chains C,I or D,J) indicated as trimeric in remark 350.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Thermolysin / / Thermostable neutral proteinase


Mass: 34360.336 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bacillus thermoproteolyticus (bacteria) / References: UniProt: P00800, thermolysin

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Inducible metalloproteinase inhibitor ... , 2 types, 4 molecules CDIJ

#2: Protein/peptide Inducible metalloproteinase inhibitor protein / IMPI alpha


Mass: 4286.869 Da / Num. of mol.: 2 / Fragment: UNP residues 19-56
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Galleria mellonella (greater wax moth) / Gene: IMPI / Plasmid: pET-32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Origami2 / References: UniProt: P82176
#3: Protein/peptide Inducible metalloproteinase inhibitor protein / IMPI alpha


Mass: 3684.299 Da / Num. of mol.: 2 / Fragment: UNP residues 57-88
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Galleria mellonella (greater wax moth) / Gene: IMPI / Plasmid: pET-32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Origami2 / References: UniProt: P82176

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Non-polymers , 5 types, 623 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ZN / ZINC ION


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


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 610 / 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: 1.95 Å3/Da / Density % sol: 36.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% w/v PEG 4000, 0.2 M sodium acetate, 0.1 M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 25, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 59746 / Num. obs: 59746 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.079
Reflection shellResolution: 1.8→1.9 Å / Rmerge(I) obs: 0.079 / Mean I/σ(I) obs: 20.3 / Num. unique all: 59746 / % possible all: 99.5

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Processing

Software
NameVersionClassification
ProDCdata collection
PHASERphasing
REFMAC5.5.0102refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2TMN

2tmn


Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 6.423 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1931 793 1.3 %RANDOM
Rwork0.15863 ---
all0.15911 59746 --
obs0.15911 58951 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.338 Å2
Baniso -1Baniso -2Baniso -3
1-2.23 Å20 Å20.23 Å2
2---1.06 Å20 Å2
3----1.17 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5842 0 28 610 6480
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0216031
X-RAY DIFFRACTIONr_bond_other_d0.0010.023860
X-RAY DIFFRACTIONr_angle_refined_deg1.3141.9318167
X-RAY DIFFRACTIONr_angle_other_deg0.90839388
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0365752
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.04924.698298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.52715888
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6261524
X-RAY DIFFRACTIONr_chiral_restr0.0820.2866
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026910
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021256
X-RAY DIFFRACTIONr_mcbond_it0.6391.53752
X-RAY DIFFRACTIONr_mcbond_other0.1831.51576
X-RAY DIFFRACTIONr_mcangle_it1.06525979
X-RAY DIFFRACTIONr_scbond_it1.76132279
X-RAY DIFFRACTIONr_scangle_it2.7254.52188
LS refinement shellResolution: 1.803→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 49 -
Rwork0.207 4150 -
obs--94.81 %
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)
11.01070.27850.43910.8266-0.32141.4555-0.05160.0185-0.0426-0.0045-0.019-0.1282-0.036-0.03190.07050.0361-0.02040.01980.074-0.02110.147522.20221.50538.712
20.94290.0458-0.71590.28950.28341.67840.0125-0.05620.02940.0419-0.03440.09120.0520.01840.02190.1401-0.0586-0.01070.15240.02460.14581.87717.88684.736
32.71912.04470.83912.8371.44741.10420.17150.185-0.0442-1.145-0.23470.8176-0.0911-0.10430.06310.16530.0618-0.08460.1916-0.00880.22676.060.32933.915
42.71983.413-1.88116.7045-2.20851.66640.1606-0.03910.0984-1.3812-0.2265-0.63670.027-0.01490.06590.31280.02630.10690.21490.01060.182816.67339.58980.018
50.20260.095-0.16820.1736-0.02070.650.0014-0.0144-0.02280.0255-0.014-0.01820.0082-0.01930.01250.1991-0.0116-0.01450.23150.00670.283113.1919.09156.367
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 316
2X-RAY DIFFRACTION1A999
3X-RAY DIFFRACTION1A998
4X-RAY DIFFRACTION1A997
5X-RAY DIFFRACTION1A996
6X-RAY DIFFRACTION1A995
7X-RAY DIFFRACTION2B1 - 316
8X-RAY DIFFRACTION2B999
9X-RAY DIFFRACTION2B998
10X-RAY DIFFRACTION2B997
11X-RAY DIFFRACTION2B996
12X-RAY DIFFRACTION2B995
13X-RAY DIFFRACTION3I57 - 86
14X-RAY DIFFRACTION3C22 - 56
15X-RAY DIFFRACTION4J57 - 85
16X-RAY DIFFRACTION4D23 - 56
17X-RAY DIFFRACTION5C595 - 1112
18X-RAY DIFFRACTION5D762 - 1101
19X-RAY DIFFRACTION5I501
20X-RAY DIFFRACTION5J853 - 1108

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