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- PDB-3lac: Crystal structure of Bacillus anthracis pyrrolidone-carboxylate p... -

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Basic information

Entry
Database: PDB / ID: 3lac
TitleCrystal structure of Bacillus anthracis pyrrolidone-carboxylate peptidase, pcP
ComponentsPyrrolidone-carboxylate peptidase
KeywordsHYDROLASE / alpha beta class / three layer sandwich / Bacillus anthracis / CSGID / Protease / Thiol protease / Structural Genomics / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


pyroglutamyl-peptidase I / pyroglutamyl-peptidase activity / proteolysis / cytosol
Similarity search - Function
Pyroglutamyl peptidase I, bacterial-type / Pyroglutamyl peptidase I, Glu active site / Pyrrolidone-carboxylate peptidase glutamic acid active site. / Peptidase C15, pyroglutamyl peptidase I-like / Pyroglutamyl peptidase I, Cys active site / Pyrrolidone-carboxylate peptidase cysteine active site. / Peptidase C15, pyroglutamyl peptidase I / Peptidase C15, pyroglutamyl peptidase I-like / Peptidase C15, pyroglutamyl peptidase I-like superfamily / Pyroglutamyl peptidase ...Pyroglutamyl peptidase I, bacterial-type / Pyroglutamyl peptidase I, Glu active site / Pyrrolidone-carboxylate peptidase glutamic acid active site. / Peptidase C15, pyroglutamyl peptidase I-like / Pyroglutamyl peptidase I, Cys active site / Pyrrolidone-carboxylate peptidase cysteine active site. / Peptidase C15, pyroglutamyl peptidase I / Peptidase C15, pyroglutamyl peptidase I-like / Peptidase C15, pyroglutamyl peptidase I-like superfamily / Pyroglutamyl peptidase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Pyrrolidone-carboxylate peptidase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsAnderson, S.M. / Wawrzak, Z. / Onopriyenko, O. / Hasseman, J. / Edwards, A. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal structure of Bacillus anthracis pyrrolidone-carboxylate peptidase, pcP
Authors: Anderson, S.M. / Wawrzak, Z. / Onopriyenko, O. / Hasseman, J. / Edwards, A. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJan 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 14, 2011Group: Database references / Structure summary
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyrrolidone-carboxylate peptidase
B: Pyrrolidone-carboxylate peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,58013
Polymers47,5772
Non-polymers1,00411
Water5,170287
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Pyrrolidone-carboxylate peptidase
B: Pyrrolidone-carboxylate peptidase
hetero molecules

A: Pyrrolidone-carboxylate peptidase
B: Pyrrolidone-carboxylate peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,16126
Polymers95,1534
Non-polymers2,00722
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_656-x+1,y,-z+11
Buried area7900 Å2
ΔGint-29 kcal/mol
Surface area34500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.55, 78.55, 141.04
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11B-227-

HOH

21B-228-

HOH

31B-290-

HOH

41B-376-

HOH

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Components

#1: Protein Pyrrolidone-carboxylate peptidase / 5-oxoprolyl-peptidase / Pyroglutamyl-peptidase I / PGP-I / Pyrase


Mass: 23788.357 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames Ancestor / Gene: pcp, BA_3090, GBAA_3090, BAS2875 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q81NT5, pyroglutamyl-peptidase I
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.29 Å3/Da / Density % sol: 46.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% PEG 3350, 1% PEG 5KMME, 200mM magnesium chloride, 100mM Tris pH 8.5, 0.5% Tacsimate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 29, 2009 / Details: beryllium lens
RadiationMonochromator: C(111) diamond laue monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2→34.3 Å / Num. all: 30826 / Num. obs: 30518 / % possible obs: 99 % / Observed criterion σ(F): 1.7 / Observed criterion σ(I): 3 / Redundancy: 10.5 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 17.8
Reflection shellResolution: 2→2.07 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.526 / Mean I/σ(I) obs: 3 / Num. unique all: 3040 / % possible all: 93.8

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.005data extraction
BLU-MAXdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2→34.3 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.23 / WRfactor Rwork: 0.189 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.871 / SU B: 8.287 / SU ML: 0.107 / SU R Cruickshank DPI: 0.18 / SU Rfree: 0.159 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 3 / ESU R: 0.18 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1538 5 %RANDOM
Rwork0.181 ---
all0.183 30826 --
obs0.183 30484 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 91.65 Å2 / Biso mean: 16.685 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å2-0 Å2-0 Å2
2--0.09 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 2→34.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3154 0 65 287 3506
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223307
X-RAY DIFFRACTIONr_angle_refined_deg1.6461.984464
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.6065.096416
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.66425.188133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.74515567
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5211511
X-RAY DIFFRACTIONr_chiral_restr0.1180.2503
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212427
X-RAY DIFFRACTIONr_mcbond_it1.5261.52043
X-RAY DIFFRACTIONr_mcangle_it2.3923334
X-RAY DIFFRACTIONr_scbond_it4.231264
X-RAY DIFFRACTIONr_scangle_it6.2794.51127
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 92 -
Rwork0.217 1947 -
all-2039 -
obs-1832 91.93 %
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)
10.49380.20890.27480.88870.04791.8416-0.0709-0.03620.07760.1022-0.02880.1066-0.4262-0.31110.09970.18440.1067-0.02860.1708-0.05050.171121.12970.82283.691
20.65340.2693-0.11381.66220.14890.6353-0.10990.02140.1254-0.0273-0.10640.1212-0.1962-0.29570.21640.14550.1025-0.07440.2652-0.03830.193917.36767.47273.871
33.1263-0.96881.13390.8640.09941.4602-0.0993-0.1290.2943-0.0140.0461-0.0943-0.41230.00130.05320.30270.0362-0.06380.078-0.00870.160431.9373.23673.467
40.2836-0.22060.22850.91220.14741.29220.006-0.04950.061-0.0623-0.04680.02320.1047-0.30070.04070.0316-0.0370.01960.3358-0.00790.140516.98639.98867.327
50.1056-0.3020.03311.47930.1450.7375-0.0595-0.08060.03040.1149-0.04410.03240.0694-0.42280.10350.06540.0070.00310.4281-0.03050.157418.34243.73577.904
62.28760.9032-1.4790.8815-0.75432.7306-0.06310.0707-0.1318-0.0761-0.0179-0.08220.1266-0.11290.0810.0858-0.00470.00560.1997-0.00620.144331.02637.68571.708
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 110
2X-RAY DIFFRACTION2A111 - 167
3X-RAY DIFFRACTION3A168 - 204
4X-RAY DIFFRACTION4B3 - 110
5X-RAY DIFFRACTION5B111 - 167
6X-RAY DIFFRACTION6B168 - 204

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