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- PDB-4bp8: Oligopeptidase B from Trypanosoma brucei - open form -

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Basic information

Entry
Database: PDB / ID: 4bp8
TitleOligopeptidase B from Trypanosoma brucei - open form
ComponentsOLIGOPEPTIDASE B
KeywordsHYDROLASE / PROLYL OLIGOPEPTIDASE / CATALYTIC REGULATION / INDUCED FIT
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / serine-type endopeptidase activity / proteolysis / cytoplasm
Similarity search - Function
Prolyl oligopeptidase, N-terminal domain / Peptidase S9A, prolyl oligopeptidase / Peptidase S9A, N-terminal domain / Prolyl oligopeptidase, N-terminal beta-propeller domain / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / 7 Propeller / Methylamine Dehydrogenase; Chain H / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold ...Prolyl oligopeptidase, N-terminal domain / Peptidase S9A, prolyl oligopeptidase / Peptidase S9A, N-terminal domain / Prolyl oligopeptidase, N-terminal beta-propeller domain / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / 7 Propeller / Methylamine Dehydrogenase; Chain H / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Prolyl endopeptidase
Similarity search - Component
Biological speciesTRYPANOSOMA BRUCEI (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsCanning, P. / Rea, D. / Morty, R. / Fulop, V.
CitationJournal: Plos One / Year: 2013
Title: Crystal Structures of Trypanosoma Brucei Oligopeptidase B Broaden the Paradigm of Catalytic Regulation in Prolyl Oligopeptidase Family Enzymes.
Authors: Canning, P. / Rea, D. / Morty, R.E. / Fulop, V.
History
DepositionMay 23, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: OLIGOPEPTIDASE B
B: OLIGOPEPTIDASE B


Theoretical massNumber of molelcules
Total (without water)163,2702
Polymers163,2702
Non-polymers00
Water14,016778
1
A: OLIGOPEPTIDASE B


Theoretical massNumber of molelcules
Total (without water)81,6351
Polymers81,6351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: OLIGOPEPTIDASE B


Theoretical massNumber of molelcules
Total (without water)81,6351
Polymers81,6351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)124.140, 124.140, 249.140
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein OLIGOPEPTIDASE B /


Mass: 81634.828 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRYPANOSOMA BRUCEI (eukaryote) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PRARE / References: UniProt: O76728, EC: 3.4.21.83
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 778 / 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: 2.88 Å3/Da / Density % sol: 57 % / Description: NONE
Crystal growpH: 9
Details: 9% (W/V) POLYETHYLENE GLYCOL 6000, 1M LITHIUM CHLORIDE, 100MM BIS-TRIS PROPANE, PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9789
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 2, 2008 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.4→66 Å / Num. obs: 86984 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 34.6 % / Biso Wilson estimate: 53.3 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 18.6
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 22.2 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 2 / % possible all: 95.6

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RESOLVEphasing
REFMAC5.5.0109refinement
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.4→65.73 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.926 / SU B: 17.257 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R: 0.263 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.23885 3521 4 %RANDOM
Rwork0.18402 ---
obs0.18625 83463 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.311 Å2
Baniso -1Baniso -2Baniso -3
1-1.95 Å20.98 Å20 Å2
2--1.95 Å20 Å2
3----2.93 Å2
Refinement stepCycle: LAST / Resolution: 2.4→65.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11302 0 0 778 12080
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02211578
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7211.95915712
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.63951422
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.22623.259540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.324151944
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6881592
X-RAY DIFFRACTIONr_chiral_restr0.1320.21708
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0218880
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.6771.57092
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.325211486
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.32234486
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7544.54226
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 237 -
Rwork0.333 5723 -
obs--93.48 %
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)
10.71570.30850.11911.488-0.42521.43220.2286-0.092-0.27650.0937-0.0380.1160.3832-0.146-0.19060.2023-0.0261-0.06890.19620.04570.200154.182434.56557.5539
22.3549-0.20390.09820.3787-0.06610.84220.0742-0.35330.23630.0849-0.0427-0.044-0.0802-0.0016-0.03160.1719-0.09720.02950.1556-0.09060.073741.558372.045776.7906
30.74390.24460.11040.66890.05870.81460.1538-0.1333-0.0120.1251-0.0952-0.0470.0303-0.012-0.05850.043-0.0299-0.01150.15410.03790.03962.392749.803759.5682
41.0354-0.24440.48920.9160.19542.07050.19120.1663-0.1731-0.1258-0.05660.00140.36940.0465-0.13450.09930.0387-0.03050.1429-0.00350.052766.29940.432720.2049
52.20180.2871-0.1250.6163-0.06880.90380.03420.12780.2793-0.09450.02880.0794-0.1938-0.016-0.0630.18970.09290.04950.10380.09360.122778.957382.287213.9637
60.7719-0.36270.13770.7067-0.00720.90410.10590.1770.0664-0.0869-0.07640.0841-0.0364-0.0502-0.02950.05140.0621-0.01890.17770.04160.072358.222455.764722.9658
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 86
2X-RAY DIFFRACTION2A87 - 441
3X-RAY DIFFRACTION3A442 - 714
4X-RAY DIFFRACTION4B3 - 86
5X-RAY DIFFRACTION5B87 - 441
6X-RAY DIFFRACTION6B442 - 714

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