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- PDB-3ife: 1.55 Angstrom Resolution Crystal Structure of Peptidase T (pepT-1... -

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Basic information

Entry
Database: PDB / ID: 3ife
Title1.55 Angstrom Resolution Crystal Structure of Peptidase T (pepT-1) from Bacillus anthracis str. 'Ames Ancestor'.
ComponentsPeptidase TTripeptide aminopeptidase
KeywordsHYDROLASE / peptidase T / pepT-1 / metallopeptidase / Aminopeptidase / Metal-binding / Metalloprotease / Protease / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


tripeptide aminopeptidase / tripeptide aminopeptidase activity / peptide catabolic process / metallopeptidase activity / proteolysis / zinc ion binding / cytoplasm
Similarity search - Function
Peptidase M20B, tripeptide aminopeptidase / ArgE / dapE / ACY1 / CPG2 / yscS family signature 1. / ArgE / dapE / ACY1 / CPG2 / yscS family signature 2. / ArgE/DapE/ACY1/CPG2/YscS, conserved site / Alpha-Beta Plaits - #360 / Peptidase M20, dimerisation domain / Bacterial exopeptidase dimerisation domain / Peptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40 ...Peptidase M20B, tripeptide aminopeptidase / ArgE / dapE / ACY1 / CPG2 / yscS family signature 1. / ArgE / dapE / ACY1 / CPG2 / yscS family signature 2. / ArgE/DapE/ACY1/CPG2/YscS, conserved site / Alpha-Beta Plaits - #360 / Peptidase M20, dimerisation domain / Bacterial exopeptidase dimerisation domain / Peptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40 / Zn peptidases / Aminopeptidase / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
sucrose / Peptidase T
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsMinasov, G. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: 1.55 Angstrom Resolution Crystal Structure of Peptidase T (pepT-1) from Bacillus anthracis str. 'Ames Ancestor'.
Authors: Minasov, G. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJul 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _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.ptnr2_label_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.value / _struct_asym.entity_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidase T
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7338
Polymers48,7021
Non-polymers1,0317
Water10,557586
1
A: Peptidase T
hetero molecules

A: Peptidase T
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,46616
Polymers97,4052
Non-polymers2,06114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area5440 Å2
ΔGint-250 kcal/mol
Surface area34970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.216, 142.739, 40.993
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein / Sugars , 2 types, 3 molecules A

#1: Protein Peptidase T / Tripeptide aminopeptidase / Tripeptide aminopeptidase / Aminotripeptidase / Tripeptidase


Mass: 48702.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames Ancestor / Gene: BAS3588, BA_3872, GBAA_3872, pepT, pepT-1 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: Q81WU4, tripeptide aminopeptidase
#2: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose /


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 591 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 586 / 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: 2.68 Å3/Da / Density % sol: 54.1 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein solution: 7.5mg/mL, 0.25M NaCl, Tris-HCl pH(8.3); Screen solution: JCSG+, E2, 0.2M NaCl, 2M Ammonium sulfate, 0.1M Na-Cacodilate pH(6.5) VAPOR DIFFUSION, SITTING DROP, temperature ...Details: Protein solution: 7.5mg/mL, 0.25M NaCl, Tris-HCl pH(8.3); Screen solution: JCSG+, E2, 0.2M NaCl, 2M Ammonium sulfate, 0.1M Na-Cacodilate pH(6.5) VAPOR DIFFUSION, SITTING DROP, temperature 295K; Cryo: 25% Sucrose, 1.8M Ammonium sulfate.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 22, 2009 / Details: Beryllium lenses
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.55→30 Å / Num. all: 77209 / Num. obs: 77209 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 25.8
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.554 / Mean I/σ(I) obs: 3.3 / Num. unique all: 3814 / % possible all: 99.3

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
CRANKphasing
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1fno

1fno


Resolution: 1.55→29.11 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.967 / SU B: 2.442 / SU ML: 0.041 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic, individual. / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17173 3863 5 %RANDOM
Rwork0.14836 ---
all0.14954 73110 --
obs0.14954 73110 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.404 Å2
Baniso -1Baniso -2Baniso -3
1--1.09 Å20 Å20 Å2
2---0.36 Å2-0 Å2
3---1.46 Å2
Refinement stepCycle: LAST / Resolution: 1.55→29.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3282 0 59 586 3927
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223762
X-RAY DIFFRACTIONr_bond_other_d0.0010.022497
X-RAY DIFFRACTIONr_angle_refined_deg1.4931.9765149
X-RAY DIFFRACTIONr_angle_other_deg0.87936167
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.195487
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.92525.751193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.07915650
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6611514
X-RAY DIFFRACTIONr_chiral_restr0.0980.2554
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214355
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02725
X-RAY DIFFRACTIONr_mcbond_it0.8541.52272
X-RAY DIFFRACTIONr_mcbond_other0.2881.5917
X-RAY DIFFRACTIONr_mcangle_it1.48123721
X-RAY DIFFRACTIONr_scbond_it2.66431490
X-RAY DIFFRACTIONr_scangle_it4.3294.51422
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.215 265 -
Rwork0.2 5361 -
obs-5361 99.63 %
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)
12.31270.3113-0.17111.06730.48811.1619-0.11710.3374-0.1037-0.05460.08150.0433-0.0643-0.08120.03570.080.0152-0.00380.1451-0.04340.018462.549935.04878.2174
21.87680.15680.01150.45140.0610.6878-0.0610.0881-0.24040.03030.01-0.01780.0276-0.03250.0510.06470.0250.00440.0574-0.02670.038163.518532.744217.3071
30.9817-1.2987-0.18842.34360.22170.2524-0.0537-0.08190.05190.0820.0412-0.2124-0.0122-0.01420.01250.05930.0091-0.00390.0441-0.00010.040388.543416.023633.083
41.4863-0.02030.19240.774-0.04210.5475-0.0556-0.0647-0.1190.10280.0050.0138-0-0.00180.05060.08140.02010.00270.0555-0.0080.02266.45234.035825.3137
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-5 - 50
2X-RAY DIFFRACTION2A51 - 207
3X-RAY DIFFRACTION3A208 - 349
4X-RAY DIFFRACTION4A350 - 410

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