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- PDB-3bb7: Structure of Prevotella intermedia prointerpain A fragment 39-359... -

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Basic information

Entry
Database: PDB / ID: 3bb7
TitleStructure of Prevotella intermedia prointerpain A fragment 39-359 (mutant C154A)
Componentsinterpain A
KeywordsHYDROLASE / cysteine protease / zymogen activation / bacterial odontopathogen
Function / homology
Function and homology information


cysteine-type peptidase activity / proteolysis
Similarity search - Function
MBG domain, YGX type / MBG domain (YGX type) / Peptidase C10 family / Protein Binding, DinI Protein; Chain A / Peptidase C10, streptopain superfmaily / Spi protease inhibitor / Spi protease inhibitor / Peptidase C10, streptopain / Peptidase C10 family / Streptopain (SpeB) ...MBG domain, YGX type / MBG domain (YGX type) / Peptidase C10 family / Protein Binding, DinI Protein; Chain A / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPrevotella intermedia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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: 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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


Theoretical massNumber of molelcules
Total (without water)35,0631
Polymers35,0631
Non-polymers00
Water6,666370
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)128.870, 38.810, 78.140
Angle α, β, γ (deg.)90.00, 127.26, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein interpain A


Mass: 35062.934 Da / Num. of mol.: 1 / Fragment: UNP residues 84-403 / Mutation: C154A
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / 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: 2.22 Å3/Da / Density % sol: 44.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10% polyethylene glycol 3000, 0.2M magnesium chloride, 0.1M sodium cacodylate, pH6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9763 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: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.5→39.07 Å / Num. all: 49377 / Num. obs: 49377 / % possible obs: 99.5 % / Observed criterion σ(I): 1.5 / Redundancy: 7 % / Biso Wilson estimate: 13.9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.4
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.409 / Mean I/σ(I) obs: 5.3 / % possible all: 97.4

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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 1DKI

1dki


Resolution: 1.5→39.07 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.412 / SU ML: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.079 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: TLS GROUP 1 CORRESPONDS TO CHAIN A MAIN CHAIN ATOMS; TLS GROUP 2 CORRESPONDS TO CHAIN A SIDE CHAIN ATOMS.
RfactorNum. reflection% reflectionSelection details
Rfree0.19338 747 1.5 %RANDOM
Rwork0.15502 ---
all0.1556 48630 --
obs0.1556 48630 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: 15.895 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å20.22 Å2
2--0.42 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.5→39.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2428 0 0 370 2798
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222516
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3991.9363428
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2665312
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.01724.914116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.15915387
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.445157
X-RAY DIFFRACTIONr_chiral_restr0.10.2370
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021950
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1960.21198
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.21750
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2266
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2270.244
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1750.231
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.361.51587
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.98622504
X-RAY DIFFRACTIONr_scbond_it2.80331086
X-RAY DIFFRACTIONr_scangle_it3.8774.5924
X-RAY DIFFRACTIONr_rigid_bond_restr1.5732673
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded2.92632452
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 40 -
Rwork0.167 3375 -
obs--94.73 %
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)
10.4828-0.04590.09710.2159-0.00060.33190.016-0.0575-0.02010.02710.0140.00310.00820.0002-0.03-0.0105-0.0016-0.0014-0.05190.0114-0.0473-10.027-1.9516.136
20.5958-0.010.1530.24530.02010.38580.0095-0.0598-0.02550.03320.01430.00520.01050.01-0.0239-0.0008-0.00190.0003-0.0360.0107-0.0371-9.737-1.94416.27
30.73520.01090.19950.21750.07160.58220.0268-0.0257-0.00550.040.00330.0034-0.00340.0018-0.03010.03920.00150.003-0.0060.01280.0177-12.004-2.3513.824
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA39 - 2941 - 256
2X-RAY DIFFRACTION1AA302 - 359264 - 321
3X-RAY DIFFRACTION2AA39 - 2941 - 256
4X-RAY DIFFRACTION2AA302 - 359264 - 321
5X-RAY DIFFRACTION3AB501 - 8701 - 370

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