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- PDB-3bba: Structure of active wild-type Prevotella intermedia interpain A c... -

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Basic information

Entry
Database: PDB / ID: 3bba
TitleStructure of active wild-type Prevotella intermedia interpain A cysteine protease
Componentsinterpain A
KeywordsHYDROLASE / Prevotella intermedia / zymogen activation / cysteine protease
Function / homology
Function and homology information


cysteine-type peptidase activity / proteolysis
Similarity search - Function
MBG domain, YGX type / MBG domain (YGX type) / Peptidase C10, streptopain superfmaily / Spi protease inhibitor / Spi protease inhibitor / Peptidase C10, streptopain / Peptidase C10 family / Streptopain (SpeB) / BspA type Leucine rich repeat region / BspA type Leucine rich repeat region (6 copies) ...MBG domain, YGX type / MBG domain (YGX type) / Peptidase C10, streptopain superfmaily / Spi protease inhibitor / Spi protease inhibitor / Peptidase C10, streptopain / Peptidase C10 family / Streptopain (SpeB) / BspA type Leucine rich repeat region / BspA type Leucine rich repeat region (6 copies) / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Leucine-rich repeat domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesPrevotella intermedia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsMallorqui-Fernandez, N. / Manandhar, S.P. / Mallorqui-Fernandez, G. / Uson, I. / Wawrzonek, K. / Kantyka, T. / Sola, M. / Thogersen, I.B. / Enghild, J.J. / Potempa, J. / Gomis-Ruth, F.X.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: A New Autocatalytic Activation Mechanism for Cysteine Proteases Revealed by Prevotella intermedia Interpain A
Authors: Mallorqui-Fernandez, N. / Manandhar, S.P. / Mallorqui-Fernandez, G. / Uson, I. / Wawrzonek, K. / Kantyka, T. / Sola, M. / Thogersen, I.B. / Enghild, J.J. / Potempa, J. / Gomis-Ruth, F.X.
History
DepositionNov 9, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 20, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: interpain A
B: interpain A


Theoretical massNumber of molelcules
Total (without water)54,6992
Polymers54,6992
Non-polymers00
Water0
1
A: interpain A


Theoretical massNumber of molelcules
Total (without water)27,3491
Polymers27,3491
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: interpain A


Theoretical massNumber of molelcules
Total (without water)27,3491
Polymers27,3491
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)129.241, 129.241, 81.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B

NCS domain segments:

Ens-ID: 1 / Refine code: 2

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALSERSERAA112 - 2951 - 184
21VALVALSERSERBB112 - 2951 - 184
32GLYGLYTYRTYRAA304 - 356193 - 245
42GLYGLYTYRTYRBB304 - 356193 - 245

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Components

#1: Protein interpain A


Mass: 27349.389 Da / Num. of mol.: 2 / Fragment: UNP residues 156-403
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Prevotella intermedia (bacteria) / Gene: PIN0048 / Plasmid: pET24d(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLysS / References: UniProt: A9J7N5

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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: 3.13 Å3/Da / Density % sol: 60.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 28% PEG 4000, 0.2M magnesium chloride, 30% xylitol, 0.1M Tris HCl, pH8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 16, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 3.2→47.25 Å / Num. all: 13017 / Num. obs: 13017 / % possible obs: 99 % / Observed criterion σ(I): 1.5 / Redundancy: 7.9 % / Biso Wilson estimate: 46.8 Å2 / Rmerge(I) obs: 0.329 / Net I/σ(I): 6.2
Reflection shellResolution: 3.2→3.4 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.897 / Mean I/σ(I) obs: 1.9 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BB7

3bb7


Resolution: 3.2→47.25 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.881 / SU B: 60.07 / SU ML: 0.418 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.492 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26117 570 4.8 %RANDOM
Rwork0.20725 ---
all0.20977 11333 --
obs0.20977 11333 99.72 %-
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: 56.898 Å2
Baniso -1Baniso -2Baniso -3
1-3.01 Å20 Å20 Å2
2--3.01 Å20 Å2
3----6.02 Å2
Refinement stepCycle: LAST / Resolution: 3.2→47.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3797 0 0 0 3797
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223901
X-RAY DIFFRACTIONr_bond_other_d0.0020.022506
X-RAY DIFFRACTIONr_angle_refined_deg1.311.9375314
X-RAY DIFFRACTIONr_angle_other_deg0.88536113
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.345494
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.59924.743175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.95215574
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2521510
X-RAY DIFFRACTIONr_chiral_restr0.0690.2559
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024469
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02803
X-RAY DIFFRACTIONr_nbd_refined0.2220.2928
X-RAY DIFFRACTIONr_nbd_other0.1910.22589
X-RAY DIFFRACTIONr_nbtor_refined0.1970.22013
X-RAY DIFFRACTIONr_nbtor_other0.0890.22017
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.293
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0410.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2010.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1780.251
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_it0.2771.53086
X-RAY DIFFRACTIONr_mcbond_other0.0581.51025
X-RAY DIFFRACTIONr_mcangle_it0.37823905
X-RAY DIFFRACTIONr_scbond_it0.65431807
X-RAY DIFFRACTIONr_scangle_it0.9954.51409
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1385tight positional0.040.05
1643medium positional0.30.5
1385tight thermal0.050.5
1643medium thermal0.282
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.434 37 -
Rwork0.376 807 -
obs--98.14 %
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)
13.76521.2812-1.3391.1702-0.65252.40720.0125-0.5051-0.3515-0.1841-0.0401-0.11240.13110.01210.0276-0.1776-0.2475-0.03380.01540.0994-0.148852.358689.773338.5684
217.07010.86764.89064.0981-0.60146.02860.41780.6747-0.6147-1.18170.4531-0.1448-1.85220.1862-0.87090.1766-0.4431-0.10530.1243-0.06580.047136.388986.242922.5994
33.9154-0.30090.09273.0962-1.82693.8774-0.1889-0.4282-0.26610.1133-0.1698-0.3401-0.25770.31040.3587-0.3646-0.09270.0659-0.27760.1013-0.261216.241176.849250.5481
423.5051-18.689310.591324.068525.562130.18813.2547-1.91421.9312-0.337-3.2001-3.6536-3.4354-4.7987-0.05460.7618-0.77450.020.51320.00250.341313.033189.817668.4017
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA112 - 2941 - 183
2X-RAY DIFFRACTION1AA304 - 357193 - 246
3X-RAY DIFFRACTION2AA295 - 303184 - 192
4X-RAY DIFFRACTION3BB112 - 2941 - 183
5X-RAY DIFFRACTION3BB304 - 361193 - 250
6X-RAY DIFFRACTION4BB295 - 303184 - 192

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