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- PDB-3tav: Crystal structure of a Methionine Aminopeptidase from Mycobacteri... -

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Basic information

Entry
Database: PDB / ID: 3tav
TitleCrystal structure of a Methionine Aminopeptidase from Mycobacterium abscessus
ComponentsMethionine aminopeptidase
KeywordsHYDROLASE / SSGCID / Seattle Structural Genomics Center for Infectious Disease / protease / auto-catalytic removal of tag / metalloexopeptidase / no anomalous signal indicates magnesium ions in active site / cobalt binding / M24A family
Function / homology
Function and homology information


: / methionyl aminopeptidase / metalloaminopeptidase activity / metal ion binding
Similarity search - Function
Peptidase M24A, methionine aminopeptidase, subfamily 1 / Peptidase M24, methionine aminopeptidase / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
(2S)-2-hydroxybutanedioic acid / D-MALATE / Methionine aminopeptidase
Similarity search - Component
Biological speciesMycobacterium abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 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
DepositionAug 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Feb 28, 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_asym_id / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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: Methionine aminopeptidase
B: Methionine aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,89713
Polymers59,3792
Non-polymers51811
Water5,278293
1
A: Methionine aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0657
Polymers29,6891
Non-polymers3756
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Methionine aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8326
Polymers29,6891
Non-polymers1435
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Methionine aminopeptidase
hetero molecules

B: Methionine aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,89713
Polymers59,3792
Non-polymers51811
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_565x-y,-y+1,-z+1/31
Buried area3630 Å2
ΔGint-108 kcal/mol
Surface area18820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.640, 119.640, 96.190
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Methionine aminopeptidase


Mass: 29689.469 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium abscessus (bacteria) / Strain: DSM 44196 / Gene: MAB_3782c / Production host: Escherichia coli (E. coli) / References: UniProt: B1MGB2, methionyl aminopeptidase

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Non-polymers , 6 types, 304 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#6: Chemical ChemComp-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 3.35 Å3/Da / Density % sol: 63.25 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: MyabA.01548.b.A1 PS01037 at 56.7 mg/mL with full 21 aa tag against JCSG + f9, 2.4 M Na malonate with 25% ethylene glycol as cryo-protectant, crystal tracking ID 222124f9, pH 7.5, VAPOR ...Details: MyabA.01548.b.A1 PS01037 at 56.7 mg/mL with full 21 aa tag against JCSG + f9, 2.4 M Na malonate with 25% ethylene glycol as cryo-protectant, crystal tracking ID 222124f9, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979175 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979175 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 43615 / Num. obs: 43354 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Biso Wilson estimate: 47.857 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 13.94
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
2.15-2.215.70.3853.3181773210320799.9
2.21-2.270.354.6518909309599.6
2.27-2.330.2515.75195623017100
2.33-2.40.2037.3190542942100
2.4-2.480.1758.58185242860100
2.48-2.570.169.6177252742100
2.57-2.670.13111.89172002682100
2.67-2.780.11913.2716198254399.9
2.78-2.90.10515.47156952492100
2.9-3.040.09217.0114617234099.9
3.04-3.210.07919.41138072244100
3.21-3.40.07221.07128762145100
3.4-3.630.06822.42118802022100
3.63-3.930.06322.9210840184999.9
3.93-4.30.0623.4410215174399.9
4.3-4.810.05723.999258157899.8
4.81-5.550.05223.888095138299.9
5.55-6.80.048247088119499.8
6.8-9.620.04723.41483787792.2
9.62-500.04520.8177540071.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.1 Å45.61 Å
Translation3.1 Å45.61 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.2341 / WRfactor Rwork: 0.2034 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8556 / SU B: 8.019 / SU ML: 0.109 / SU R Cruickshank DPI: 0.1681 / SU Rfree: 0.1502 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES: WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.216 2186 5 %RANDOM
Rwork0.1868 ---
obs0.1884 43330 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 84.88 Å2 / Biso mean: 48.1471 Å2 / Biso min: 32.79 Å2
Baniso -1Baniso -2Baniso -3
1--1.38 Å2-0.69 Å20 Å2
2---1.38 Å20 Å2
3---2.08 Å2
Refinement stepCycle: LAST / Resolution: 2.15→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3810 0 27 293 4130
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193909
X-RAY DIFFRACTIONr_angle_refined_deg1.4561.9585335
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0915528
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.74923.379145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.40615569
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0751527
X-RAY DIFFRACTIONr_chiral_restr0.0950.2629
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212981
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 130 -
Rwork0.269 2906 -
all-3036 -
obs--99.9 %
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)
10.513-0.0605-0.00150.3968-0.24570.4319-0.0125-0.0861-0.0091-0.0342-0.0871-0.04890.02560.04050.09960.06680.0686-0.05320.35840.00910.299647.027455.373910.7581
21.50322.44810.52949.21377.99189.9432-0.0128-0.0805-0.1383-0.6774-0.0272-0.2972-0.72870.07210.040.1430.17390.01710.40930.16160.3950.65269.1362.8071
30.89060.0416-0.06080.8436-0.17730.45610.1032-0.28270.0274-0.0249-0.1626-0.0271-0.0429-0.04940.05940.06220.0303-0.06710.4414-0.03020.220643.425760.316320.3059
44.8186-0.29720.82280.0184-0.05050.14140.0199-0.0356-0.15050.00070.00740.0080.00720.0127-0.02730.0540.0731-0.08120.4280.04790.324855.376850.092414.2714
52.89611.91751.9341.30171.32461.35230.050.1338-0.29760.00530.0331-0.12920.0026-0.0343-0.08310.01860.0370.0190.3733-0.0110.435186.423842.237816.9654
60.7259-0.0358-0.09930.80460.13370.39760.09640.06690.10450.0717-0.18270.0951-0.03690.02080.08630.0814-0.0782-0.06240.35710.02190.286872.02165.394322.0699
70.7944-0.3393-0.16151.04340.34170.23980.13240.3845-0.099-0.0325-0.20060.0405-0.02350.08330.06820.06250.0009-0.06290.53380.02230.186676.762757.09727.9782
84.54150.8279-0.0860.1512-0.01540.0036-0.00440.0367-0.1778-0.00380.0031-0.03040.002-0.02950.00130.0762-0.0625-0.09650.4511-0.01540.328764.26350.09417.7903
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 47
2X-RAY DIFFRACTION2A48 - 61
3X-RAY DIFFRACTION3A62 - 254
4X-RAY DIFFRACTION4A255 - 265
5X-RAY DIFFRACTION5B2 - 12
6X-RAY DIFFRACTION6B13 - 123
7X-RAY DIFFRACTION7B124 - 254
8X-RAY DIFFRACTION8B255 - 265

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