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- PDB-4bp9: Oligopeptidase B from Trypanosoma brucei with covalently bound an... -

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Basic information

Entry
Database: PDB / ID: 4bp9
TitleOligopeptidase B from Trypanosoma brucei with covalently bound antipain - closed form
Components
  • ANTIPAIN
  • OLIGOPEPTIDASSE B
KeywordsHYDROLASE / PROLYL OLIGOPEPTIDASE
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 ...: / 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
Antipain / : / Prolyl endopeptidase
Similarity search - Component
Biological speciesTRYPANOSOMA BRUCEI (eukaryote)
ACTINOBACTERIA (actinobacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 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
Revision 1.1Mar 19, 2014Group: Atomic model / Database references
Revision 1.2Jun 18, 2014Group: Atomic model
Revision 1.3Sep 13, 2017Group: Advisory / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_validate_polymer_linkage
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list
Revision 2.0May 15, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Polymer sequence
Category: database_PDB_caveat / diffrn_source ...database_PDB_caveat / diffrn_source / entity_poly / pdbx_seq_map_depositor_info / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _entity_poly.pdbx_seq_one_letter_code_can ..._diffrn_source.pdbx_synchrotron_site / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_seq_map_depositor_info.one_letter_code / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_validate_peptide_omega / pdbx_validate_torsion / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: OLIGOPEPTIDASSE B
B: OLIGOPEPTIDASSE B
C: OLIGOPEPTIDASSE B
D: OLIGOPEPTIDASSE B
E: OLIGOPEPTIDASSE B
F: OLIGOPEPTIDASSE B
G: ANTIPAIN
H: ANTIPAIN
I: ANTIPAIN
J: ANTIPAIN
K: ANTIPAIN
L: ANTIPAIN


Theoretical massNumber of molelcules
Total (without water)488,39012
Polymers488,39012
Non-polymers00
Water6,197344
1
A: OLIGOPEPTIDASSE B
G: ANTIPAIN


Theoretical massNumber of molelcules
Total (without water)81,3982
Polymers81,3982
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: OLIGOPEPTIDASSE B
H: ANTIPAIN


Theoretical massNumber of molelcules
Total (without water)81,3982
Polymers81,3982
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: OLIGOPEPTIDASSE B
I: ANTIPAIN


Theoretical massNumber of molelcules
Total (without water)81,3982
Polymers81,3982
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: OLIGOPEPTIDASSE B
J: ANTIPAIN


Theoretical massNumber of molelcules
Total (without water)81,3982
Polymers81,3982
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: OLIGOPEPTIDASSE B
K: ANTIPAIN


Theoretical massNumber of molelcules
Total (without water)81,3982
Polymers81,3982
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: OLIGOPEPTIDASSE B
L: ANTIPAIN


Theoretical massNumber of molelcules
Total (without water)81,3982
Polymers81,3982
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.800, 148.800, 268.000
Angle α, β, γ (deg.)90.00, 91.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
OLIGOPEPTIDASSE B


Mass: 80790.688 Da / Num. of mol.: 6
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: Protein/peptide
ANTIPAIN


Type: Oligopeptide / Class: Enzyme inhibitor / Mass: 607.725 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) ACTINOBACTERIA (actinobacteria) / References: NOR: NOR00664, Antipain
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / Source method: isolated from a natural source / Formula: H2O
Compound detailsANTIPAIN HYDROCHLORIDE IS A REVERSIBLE INHIBITOR OF SERINE/CYSTEINE PROTEASES AND SOME TRYPSIN-LIKE ...ANTIPAIN HYDROCHLORIDE IS A REVERSIBLE INHIBITOR OF SERINE/CYSTEINE PROTEASES AND SOME TRYPSIN-LIKE SERINE PROTEASES. ITS ACTION RESEMBLES LEUPEPTIN; HOWEVER, ITS PLASMIN INHIBITION IS LESS AND ITS CATHEPSIN A INHIBITION IS MORE THAN THAT OBSERVED WITH LEUPEPTIN. IT IS AN INHIBITOR OF TRYPSIN-LIKE PROTEASES (E.G. TRYPSIN, PAPAIN, CATHEPSIN B); CATHEPSIN A, A CARBOXYPEPTIDASE IS INHIBITED TOO, WHICH IS NOT TRUE FOR OTHER INHIBITORS FROM ACTINOMYCES.THE NAME IS DERIVED FROM ANTI-PAPAIN. GROUP: 1 NAME: ANTIPAIN CHAIN: G, H, I, J, K, L COMPONENT_1: PEPTIDE LIKE SEQUENCE RESIDUES 1 TO 4 DESCRIPTION: ANTIPAIN FORMS A COVALENT LINKAGE BETWEEN THE ARGINAL RESIDUE OF THE INHIBITOR AND SER RESIDUE OF THE PROTEIN.THE PROTEASE INHIBITOR ANTIPAIN INCREASES THE EFFECTIVENESSOF UV IRRADIATION ON CESSATION OF RESPIRATION AND CELL KILLING IN ESCHERICHIA COLI B/R CULTURES WITHOUT AFFECTING EXCISION OF PYRIMIDINE DIMERS. THE ACTIONS ARE SIMILAR TO THOSE CAUSED BY CYCLIC AMP IN IRRADIATED CULTURES.
Nonpolymer detailsANTIPAIN: COVALENTLY BOUND TO THE CATALYTIC SER563

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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 Å3/Da / Density % sol: 59 %
Description: STARTING MODEL IS ALSO BEING CURRENTLY DEPOSITED
Crystal growpH: 5
Details: 10 % PEG 4000, 0.2 M CALCIUM ACETATE, 0.1 M SODIUM ACETATE PH 5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9778
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 27, 2009 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2.85→59 Å / Num. obs: 127053 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 45.4 Å2 / Rmerge(I) obs: 0.22 / Net I/σ(I): 8.3
Reflection shellResolution: 2.85→3 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.12 / Mean I/σ(I) obs: 2.2 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→58.59 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.882 / SU B: 43.636 / SU ML: 0.381 / Cross valid method: THROUGHOUT / ESU R Free: 0.436 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.28074 5162 4.1 %RANDOM
Rwork0.21333 ---
obs0.21609 121891 96.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.4 Å2
Baniso -1Baniso -2Baniso -3
1--1.97 Å20 Å20.69 Å2
2--1.49 Å20 Å2
3---0.51 Å2
Refinement stepCycle: LAST / Resolution: 2.85→58.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34062 0 0 344 34406
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02234896
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6971.96647322
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1154254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.78823.2341614
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.883155814
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.51315276
X-RAY DIFFRACTIONr_chiral_restr0.1150.25136
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02126730
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_it0.3921.521210
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.774234344
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.381313686
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.3024.512978
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: 2.85→2.924 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 379 -
Rwork0.292 8894 -
obs--96.86 %
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)
11.6990.6199-0.29262.1497-0.76312.55520.19580.12530.41750.36550.18410.5994-0.5691-0.5266-0.37990.41670.1220.15760.67170.06340.338110.59121.825223.942
20.79740.0510.03120.9615-0.14611.34160.0236-0.19810.06130.26440.04920.01670.05640.1057-0.07280.43450.01750.01650.5750.0290.161730.733106.19248.746
30.69790.2719-0.10351.3464-0.06081.23120.04310.01660.09670.10.02230.03330.1256-0.0731-0.06540.3974-0.01350.03020.56190.02240.223322.66109.662220.164
41.70730.8004-0.17872.2222-0.35741.73040.10910.19830.2519-0.0253-0.050.3722-0.5191-0.299-0.05910.50180.09260.06350.57050.06220.195830.349140.463194.085
50.60990.118-0.13440.66880.03052.06830.04520.1562-0.0498-0.0502-0.0286-0.03250.01130.7632-0.01660.2849-0.01710.04620.95-0.0040.195260.203124.79182.927
60.90620.33950.00040.6838-0.06981.56490.03180.04040.02810.01670.03460.0325-0.40140.2819-0.06650.5128-0.09160.04920.64350.00730.255143.72136.632204.797
72.94130.4731.50780.90720.17743.36260.07030.0353-0.5749-0.1498-0.2024-0.13140.7459-0.40660.13210.7079-0.0160.19930.7692-0.10790.31754.78542.353216.169
80.98810.2944-0.32790.6715-0.11561.82390.01950.30420.0102-0.1385-0.04360.0142-0.4683-0.53380.02410.81870.24830.05210.81940.02320.204160.38872.649198.305
90.83210.139-0.32560.51250.21341.78250.04490.2659-0.0686-0.1575-0.1292-0.0214-0.0504-0.64420.08430.6350.10060.06150.9659-0.04210.298648.14257.761221.194
103.64220.40761.24111.14040.1893.2490.0071-0.141-0.48210.1323-0.21490.11140.97230.09140.20780.6980.12450.23270.630.12110.293765.61742.517255.153
110.9444-0.0542-0.3010.986-0.19051.87140.0269-0.20010.02990.1758-0.07540.091-0.31450.2250.04850.5627-0.07240.04170.64740.01240.190160.02572.851272.847
120.61430.1707-0.53680.53190.08432.11110.0079-0.0999-0.07870-0.13510.00470.05550.3940.12720.55410.04110.10550.77660.10210.307472.29257.815250.051
131.27760.01-1.29050.9642-0.2896.05420.16140.16440.00610.13450.01180.3237-0.5452-1.9389-0.17320.36350.12840.00731.22150.05860.2785-3.07647.468159.115
141.1442-0.0342-1.04010.6682-0.06144.7127-0.2468-0.3082-0.12460.23480.0687-0.02711.01130.420.17810.79860.11130.09870.61690.05210.245316.47231.29183.978
151.02160.1705-1.11950.6808-0.21295.1965-0.25810.1592-0.09790.06560.06420.02010.8737-0.66510.19390.6198-0.15320.10860.6742-0.05240.26018.83335.157155.353
162.10890.1485-0.75942.5497-0.08124.80520.1890.4240.2735-0.0147-0.04710.2624-1.5659-0.5421-0.14190.88110.10660.0490.65640.04880.207217.43765.923129.643
170.5034-0.0053-0.23080.856-0.13634.5782-0.0072-0.015-0.0005-0.01820.0026-0.0323-0.19261.86570.00460.2921-0.16090.0551.4549-0.06060.257346.98349.452118.503
180.81710.0084-0.46840.6648-0.21584.41240.1334-0.05150.07050.08520.0178-0.057-1.17220.842-0.15120.7467-0.28020.06750.7807-0.04090.276330.62861.755140.349
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 86
2X-RAY DIFFRACTION2A87 - 441
3X-RAY DIFFRACTION3A442 - 714
4X-RAY DIFFRACTION4B5 - 86
5X-RAY DIFFRACTION5B87 - 441
6X-RAY DIFFRACTION6B442 - 714
7X-RAY DIFFRACTION7C5 - 86
8X-RAY DIFFRACTION8C87 - 441
9X-RAY DIFFRACTION9C442 - 714
10X-RAY DIFFRACTION10D5 - 86
11X-RAY DIFFRACTION11D87 - 441
12X-RAY DIFFRACTION12D442 - 714
13X-RAY DIFFRACTION13E5 - 86
14X-RAY DIFFRACTION14E87 - 441
15X-RAY DIFFRACTION15E442 - 714
16X-RAY DIFFRACTION16F5 - 86
17X-RAY DIFFRACTION17F87 - 441
18X-RAY DIFFRACTION18F442 - 714

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