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- PDB-4on1: Crystal Structure of metalloproteinase-II from Bacteroides fragilis -

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Basic information

Entry
Database: PDB / ID: 4on1
TitleCrystal Structure of metalloproteinase-II from Bacteroides fragilis
ComponentsPutative metalloprotease II
KeywordsHYDROLASE / pathogenicity island / human pathogen / fragilysin / metalloproteinases / extracellular
Function / homology
Function and homology information


extracellular matrix / metalloendopeptidase activity / proteolysis / zinc ion binding
Similarity search - Function
Lipocalin - #470 / Fragilysin / Fragilysin, N-terminal / Fragilysin, N-terminal domain superfamily / N-terminal domain of fragilysin / Peptidase M10, metallopeptidase / Matrixin / Peptidase, metallopeptidase / Zinc-dependent metalloprotease / Collagenase (Catalytic Domain) ...Lipocalin - #470 / Fragilysin / Fragilysin, N-terminal / Fragilysin, N-terminal domain superfamily / N-terminal domain of fragilysin / Peptidase M10, metallopeptidase / Matrixin / Peptidase, metallopeptidase / Zinc-dependent metalloprotease / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / Lipocalin / Prokaryotic membrane lipoprotein lipid attachment site profile. / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Fragilysin family metalloproteinase MP-II
Similarity search - Component
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsAleshin, A.E. / Liddington, R.C. / Shiryaev, S.A. / Strongin, A.Y.
CitationJournal: Febs J. / Year: 2014
Title: Structural and functional diversity of metalloproteinases encoded by the Bacteroides fragilis pathogenicity island.
Authors: Shiryaev, S.A. / Aleshin, A.E. / Muranaka, N. / Kukreja, M. / Routenberg, D.A. / Remacle, A.G. / Liddington, R.C. / Cieplak, P. / Kozlov, I.A. / Strongin, A.Y.
History
DepositionJan 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_label_asym_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_label_asym_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

Downloads & links

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Assembly

Deposited unit
A: Putative metalloprotease II
B: Putative metalloprotease II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,0655
Polymers84,8422
Non-polymers2233
Water7,728429
1
A: Putative metalloprotease II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4872
Polymers42,4211
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative metalloprotease II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5793
Polymers42,4211
Non-polymers1582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.424, 114.395, 140.213
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative metalloprotease II


Mass: 42421.246 Da / Num. of mol.: 2 / Mutation: E352A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Plasmid: pET101 / Production host: Escherichia coli (E. coli) / References: UniProt: O68424
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 429 / 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: 2.1 Å3/Da / Density % sol: 41.42 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Well solution: 20% PEG3330, 0.2M MgCl2 Crystallization drop: 50% of 25 mM HEPES buffer, 100 mM NaCl, 4 mM CaCl2 and 50% of the well solution, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.03319 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 20, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03319 Å / Relative weight: 1
ReflectionResolution: 2.13→50 Å / Num. all: 41324 / Num. obs: 41324 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.4 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.135 / Net I/σ(I): 21
Reflection shellResolution: 2.13→2.19 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 4.8 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.13→44.319 Å / SU ML: 0.16 / σ(F): 1.34 / Phase error: 18.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2004 2064 5 %random
Rwork0.1591 ---
obs0.1612 41241 99.75 %-
all-41324 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.13→44.319 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5298 0 8 429 5735
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055413
X-RAY DIFFRACTIONf_angle_d0.9167330
X-RAY DIFFRACTIONf_dihedral_angle_d14.3291979
X-RAY DIFFRACTIONf_chiral_restr0.038814
X-RAY DIFFRACTIONf_plane_restr0.004937
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1225-2.17190.22671290.18982452X-RAY DIFFRACTION97
2.1719-2.22620.23221370.17362619X-RAY DIFFRACTION100
2.2262-2.28640.2391350.16652537X-RAY DIFFRACTION100
2.2864-2.35360.23541360.17042592X-RAY DIFFRACTION100
2.3536-2.42960.24651350.16922566X-RAY DIFFRACTION100
2.4296-2.51640.22251370.15892591X-RAY DIFFRACTION100
2.5164-2.61720.21961380.16562625X-RAY DIFFRACTION100
2.6172-2.73630.21281360.15822569X-RAY DIFFRACTION100
2.7363-2.88050.21431360.16562599X-RAY DIFFRACTION100
2.8805-3.06090.18741390.16672606X-RAY DIFFRACTION100
3.0609-3.29720.23251370.16342615X-RAY DIFFRACTION100
3.2972-3.62890.20071400.14822638X-RAY DIFFRACTION100
3.6289-4.15360.16311380.14012657X-RAY DIFFRACTION100
4.1536-5.23180.15881420.13942683X-RAY DIFFRACTION100
5.2318-44.32830.19791490.17792828X-RAY DIFFRACTION100
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)
11.22530.1819-0.11512.46410.41141.2401-0.0468-0.0552-0.16320.13030.0065-0.12920.17490.12820.00850.13940.0220.00490.10860.01430.113752.5654108.925136.7601
21.16260.2466-0.5321.9483-0.86722.32630.0423-0.10540.00290.1376-0.0574-0.0594-0.1180.1754-0.00070.0803-0.02020.00140.1-0.00940.106847.0284126.7506146.0309
30.67210.06120.06462.15251.23552.22130.0173-0.0229-0.0707-0.0523-0.06470.13680.0417-0.21290.03560.1592-0.01040.00840.17760.00520.20630.450689.7919163.6165
41.38920.1241-0.35711.7471-0.79832.42530.0273-0.023-0.0440.09860.00550.0657-0.0716-0.0386-0.02140.0928-0.0110.0110.1226-0.01740.082835.7219104.435177.3813
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 32 through 217 )
2X-RAY DIFFRACTION2chain 'A' and (resid 218 through 396 )
3X-RAY DIFFRACTION3chain 'B' and (resid 32 through 217 )
4X-RAY DIFFRACTION4chain 'B' and (resid 218 through 396 )

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