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- PDB-3nwo: Crystal structure of Proline iminopeptidase Mycobacterium smegmatis -

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Basic information

Entry
Database: PDB / ID: 3nwo
TitleCrystal structure of Proline iminopeptidase Mycobacterium smegmatis
ComponentsProline iminopeptidase
KeywordsHYDROLASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / proline iminopeptidase / Mycobacterium smegmatis / Mycobacterium
Function / homology
Function and homology information


prolyl aminopeptidase / peptidase activity / proteolysis
Similarity search - Function
Proline-specific peptidase / Peptidase S33 / : / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
prolyl aminopeptidase
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Tuberculosis (Edinb) / Year: 2015
Title: Increasing the structural coverage of tuberculosis drug targets.
Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / ...Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / Gardberg, A.S. / Choi, R. / Hewitt, S.N. / Napuli, A.J. / Myers, J. / Barrett, L.K. / Zhang, Y. / Ferrell, M. / Mundt, E. / Thompkins, K. / Tran, N. / Lyons-Abbott, S. / Abramov, A. / Sekar, A. / Serbzhinskiy, D. / Lorimer, D. / Buchko, G.W. / Stacy, R. / Stewart, L.J. / Edwards, T.E. / Van Voorhis, W.C. / Myler, P.J.
History
DepositionJul 9, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 22, 2015Group: Database references
Revision 1.3Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _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: Proline iminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3635
Polymers36,0921
Non-polymers2714
Water5,999333
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.930, 69.920, 55.630
Angle α, β, γ (deg.)90.000, 93.180, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Proline iminopeptidase / PIP


Mass: 36092.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_2681 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0QVS8, prolyl aminopeptidase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / 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: 2.1 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% PEG 3350, 0.2 M sodium citrate, 0.1 M Tris propane, pH 8.5, vapor diffusion, sitting drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: May 14, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 24228 / % possible obs: 94.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 17.989 Å2 / Rmerge(I) obs: 0.117 / Net I/σ(I): 12.87
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.8-1.850.5272.22600104955.8
1.85-1.90.4372.63823141077.6
1.9-1.950.3953.45368173097
1.95-2.010.3354.26335174499.7
2.01-2.080.2875.57230165599.5
2.08-2.150.2466.97954161599.8
2.15-2.230.2337.78425157899.7
2.23-2.320.2139.28454150499.2
2.32-2.430.18610.19094144199.9
2.43-2.550.18211.610094139499.9
2.55-2.680.15912.797671317100
2.68-2.850.14313.791891236100
2.85-3.040.11116.988811182100
3.04-3.290.09220.981381100100
3.29-3.60.0722675991020100
3.6-4.020.05634.36871915100
4.02-4.650.04838615381499.9
4.65-5.690.05631.55107676100
5.69-8.050.07624.24090546100
8.050.03553211130299.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å37.94 Å
Translation2.5 Å37.94 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→37.94 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.283 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.173 1104 5.1 %RANDOM
Rwork0.136 ---
obs0.138 21658 99.49 %-
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: 10.295 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20.17 Å2
2---0.17 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.9→37.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2304 0 17 333 2654
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0212443
X-RAY DIFFRACTIONr_bond_other_d0.0010.021598
X-RAY DIFFRACTIONr_angle_refined_deg1.4121.9283353
X-RAY DIFFRACTIONr_angle_other_deg0.95733886
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7575312
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.80323.417120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.86115345
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0891518
X-RAY DIFFRACTIONr_chiral_restr0.0890.2367
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212789
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02503
X-RAY DIFFRACTIONr_mcbond_it0.6681.51518
X-RAY DIFFRACTIONr_mcbond_other0.2081.5601
X-RAY DIFFRACTIONr_mcangle_it1.11222463
X-RAY DIFFRACTIONr_scbond_it1.9043925
X-RAY DIFFRACTIONr_scangle_it2.934.5883
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 75 -
Rwork0.199 1478 -
all-1553 -
obs--97.55 %
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)
11.09831.42290.5962.87881.77011.28740.0773-0.0478-0.05180.1729-0.1038-0.02320.1099-0.07440.02650.0451-0.0006-0.01310.0059-0.00060.019313.95151.29329.569
20.02170.0185-0.01280.16580.03850.06890.02310.00720.00230.0282-0.00810.00170.003-0.022-0.01490.0308-0.00240.00320.02680.00060.022710.89654.56417.872
30.3396-0.29380.1010.3376-0.22940.36920.011-0.0175-0.015-0.03860.0107-0.0022-0.0051-0.0178-0.02170.04170.0010.02170.01480.0030.029927.61655.367-5.196
43.03260.3711.0820.378-0.06650.5053-0.06240.16320.0638-0.08620.007-0.04670.02690.06720.05550.03960.00920.02660.03290.00670.023618.26145.9415.41
50.4398-0.1061-0.04480.19880.1250.59910.03440.00320.04-0.0224-0.0196-0.0127-0.0435-0.0167-0.01480.02550.00670.01130.0059-0.00050.017413.70367.08412.226
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 32
2X-RAY DIFFRACTION2A33 - 145
3X-RAY DIFFRACTION3A146 - 198
4X-RAY DIFFRACTION4A199 - 228
5X-RAY DIFFRACTION5A229 - 306

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