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- PDB-3p24: Structure of profragilysin-3 from Bacteroides fragilis -

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Basic information

Entry
Database: PDB / ID: 3p24
TitleStructure of profragilysin-3 from Bacteroides fragilis
ComponentsBFT-3
KeywordsHYDROLASE / metzincins / Metalloendopeptidase
Function / homology
Function and homology information


metallopeptidase activity / proteolysis / zinc ion binding
Similarity search - Function
Lipocalin - #470 / Fragilysin / Fragilysin, N-terminal / Fragilysin, N-terminal domain superfamily / N-terminal domain of fragilysin / Metallo-peptidase family M12B Reprolysin-like / Peptidase, metallopeptidase / Zinc-dependent metalloprotease / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) ...Lipocalin - #470 / Fragilysin / Fragilysin, N-terminal / Fragilysin, N-terminal domain superfamily / N-terminal domain of fragilysin / Metallo-peptidase family M12B Reprolysin-like / 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
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsGoulas, T. / Arolas, J.L. / Gomis-Ruth, F.X.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structure, function and latency regulation of a bacterial enterotoxin potentially derived from a mammalian adamalysin/ADAM xenolog.
Authors: Goulas, T. / Arolas, J.L. / Gomis-Ruth, F.X.
History
DepositionOct 1, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 21, 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: BFT-3
B: BFT-3
C: BFT-3
D: BFT-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,11719
Polymers177,7884
Non-polymers1,32915
Water20,6631147
1
A: BFT-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0678
Polymers44,4471
Non-polymers6207
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BFT-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6464
Polymers44,4471
Non-polymers2003
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: BFT-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5122
Polymers44,4471
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: BFT-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8915
Polymers44,4471
Non-polymers4444
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.740, 69.140, 158.910
Angle α, β, γ (deg.)90.00, 91.57, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
BFT-3 / Metalloprotease / Metalloprotease enterotoxin


Mass: 44446.965 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Strain: ATCC 43858 / Gene: bft-3 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): Origami-2(DE3) / References: UniProt: O86049, fragilysin

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Non-polymers , 5 types, 1162 molecules

#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-AZI / AZIDE ION / Azide


Mass: 42.020 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: N3
#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 / Water


Mass: 18.015 Da / Num. of mol.: 1147 / 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: 2.56 Å3/Da / Density % sol: 51.87 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 100mM sodium citrate dihydrate, 20% PEG 3000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0723 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 27, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 164503 / Num. obs: 164503 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.075

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Processing

Software
NameVersionClassification
ProDCdata collection
SHELXSphasing
REFMAC5.5.0102refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.156 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20436 781 50 %RANDOM
Rwork0.16971 ---
obs0.16988 163722 98.89 %-
all-164503 --
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: 33.719 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å20.05 Å2
2--0.4 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11311 0 75 1147 12533
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02211715
X-RAY DIFFRACTIONr_bond_other_d0.0010.027852
X-RAY DIFFRACTIONr_angle_refined_deg1.2711.9515860
X-RAY DIFFRACTIONr_angle_other_deg0.824319161
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.39651437
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.95224.852575
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.341151984
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9331552
X-RAY DIFFRACTIONr_chiral_restr0.080.21716
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213083
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022373
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_it0.7921.57117
X-RAY DIFFRACTIONr_mcbond_other0.1811.52900
X-RAY DIFFRACTIONr_mcangle_it1.463211487
X-RAY DIFFRACTIONr_scbond_it2.07234598
X-RAY DIFFRACTIONr_scangle_it3.3314.54362
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 57 -
Rwork0.284 11894 -
obs--97.91 %
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)
11.7654-0.2675-0.06471.470.42372.3360.01670.0033-0.24770.0489-0.0091-0.18190.28850.3297-0.00750.07450.0374-0.00290.0710.01450.160136.0047-3.41539.0304
21.2130.4346-0.09521.4212-0.12211.6543-0.0001-0.0882-0.00960.0792-0.02880.06430.00320.00190.02890.025-0.01150.00080.01340.00470.040623.33434.58255.7576
32.4332-0.77370.01161.70490.01681.8022-0.00330.27860.3047-0.1285-0.0404-0.0549-0.3034-0.15510.04370.12080.0426-0.02420.12110.02740.091513.192720.56524.1773
42.3269-0.1550.15661.95560.63592.49820.0550.3626-0.1126-0.3036-0.1095-0.0079-0.0905-0.06260.05450.14420.03480.0040.2459-0.04190.033315.74344.17649.3146
51.96620.498-0.16521.8071-0.08251.8705-0.0656-0.0872-0.24040.08360.0045-0.02310.2807-0.07470.06110.0929-0.02660.0220.02780.00870.0854.777923.641154.8728
61.8253-0.23650.01391.74410.01052.2119-0.0599-0.15990.12050.280.0392-0.0525-0.11380.04970.02070.1265-0.0037-0.01850.0652-0.01850.031857.218840.783369.5423
72.13730.1921-0.06681.93550.38042.18890.07040.08790.3415-0.0683-0.0096-0.2725-0.26230.3323-0.06080.0671-0.04840.0250.08380.04520.185176.920647.45739.159
81.5183-0.6038-0.06211.51980.09691.56250.07820.2710.0891-0.136-0.08850.0834-0.01090.01080.01030.04660.02940.00040.08810.04430.048364.619239.248723.0373
90.41890.1460.0080.23190.02810.11890.01210.02520.0050.0081-0.02080.0031-0.0016-0.00690.00870.20520.0240.00430.18390.00710.198141.369121.125241.6072
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A33 - 201
2X-RAY DIFFRACTION2A210 - 397
3X-RAY DIFFRACTION2A999
4X-RAY DIFFRACTION3B33 - 200
5X-RAY DIFFRACTION4B211 - 397
6X-RAY DIFFRACTION4B999
7X-RAY DIFFRACTION5C33 - 199
8X-RAY DIFFRACTION6C211 - 397
9X-RAY DIFFRACTION6C999
10X-RAY DIFFRACTION7D33 - 202
11X-RAY DIFFRACTION8D211 - 397
12X-RAY DIFFRACTION8D999
13X-RAY DIFFRACTION9W501 - 1658

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