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- PDB-3r9p: Crystal structure of AckA from Mycobacterium paratuberculosis ATC... -

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Basic information

Entry
Database: PDB / ID: 3r9p
TitleCrystal structure of AckA from Mycobacterium paratuberculosis ATCC BAA-968 / K-10
ComponentsAckA
KeywordsTRANSFERASE / SSGCID / seattle structural genomics center for infectious disease / acetate kinase
Function / homology
Function and homology information


acetate kinase / organic acid metabolic process / acetate kinase activity / acetyl-CoA biosynthetic process / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
Acetate/propionate kinase / Aliphatic acid kinase, short-chain, conserved site / Acetate and butyrate kinases family signature 1. / Aliphatic acid kinase, short-chain / Acetokinase family / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Acetate kinase
Similarity search - Component
Biological speciesMycobacterium avium subsp. paratuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 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
DepositionMar 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 11, 2015Group: Database references
Revision 1.3Apr 15, 2015Group: Database references
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: AckA
B: AckA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,7726
Polymers83,3182
Non-polymers4554
Water10,503583
1
A: AckA
hetero molecules

B: AckA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,7726
Polymers83,3182
Non-polymers4554
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y+1/2,-z-1/21
Buried area7180 Å2
ΔGint-30 kcal/mol
Surface area28640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.254, 99.507, 103.871
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein AckA


Mass: 41658.980 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium avium subsp. paratuberculosis (bacteria)
Strain: ATCC BAA-968 / K-10 / Gene: ackA, MAP_3886 / Production host: Escherichia coli (E. coli) / References: UniProt: Q73T33
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 583 / 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: 2.58 Å3/Da / Density % sol: 52.36 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1 MIB buffer, 25% PEG 1500, Cryo 25% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 4, 2011
RadiationMonochromator: asymmertic curved crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 68749 / % possible obs: 100 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 11.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.9-1.936.60.4431100
1.93-1.976.60.3971100
1.97-2.016.60.3241100
2.01-2.056.60.291100
2.05-2.096.60.2421100
2.09-2.146.60.2181100
2.14-2.196.60.1921100
2.19-2.256.60.1791100
2.25-2.326.60.1461100
2.32-2.396.60.1311100
2.39-2.486.60.1231100
2.48-2.586.60.1091100
2.58-2.76.60.0971100
2.7-2.846.60.091100
2.84-3.026.50.0881100
3.02-3.256.40.0851100
3.25-3.586.10.076199.9
3.58-4.096.20.0661100
4.09-5.166.20.0371100
5.16-506.30.026199.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 46.89 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å49.75 Å
Translation2.5 Å49.75 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.785 / SU ML: 0.078 / SU R Cruickshank DPI: 0.1317 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20173 3458 5 %RANDOM
Rwork0.17118 ---
obs0.17275 65029 99.56 %-
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: 31.439 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å20 Å20 Å2
2---0.07 Å20 Å2
3---0.51 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5613 0 30 583 6226
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0215799
X-RAY DIFFRACTIONr_bond_other_d0.0020.023866
X-RAY DIFFRACTIONr_angle_refined_deg1.2091.9657883
X-RAY DIFFRACTIONr_angle_other_deg0.88639369
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7765774
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.17222.45249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.51515882
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4351559
X-RAY DIFFRACTIONr_chiral_restr0.0680.2911
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216646
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021219
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_it0.6231.53771
X-RAY DIFFRACTIONr_mcbond_other0.1351.51573
X-RAY DIFFRACTIONr_mcangle_it1.14226010
X-RAY DIFFRACTIONr_scbond_it1.77332028
X-RAY DIFFRACTIONr_scangle_it2.9744.51864
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.898→1.948 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 249 -
Rwork0.198 4658 -
obs--97.77 %
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)
10.12490.0987-0.21320.2664-0.1190.6126-0.00180.04050.01860.00280.01680.03690.0631-0.1302-0.0150.0174-0.0234-0.00410.04630.01580.016619.2704-1.6858-23.1605
20.21380.0140.10830.54630.03990.1571-0.03890.02940.02930.00210.0373-0.0315-0.0323-0.00190.00160.01130.0004-0.00780.0148-0.00350.019151.5233-18.2627-17.9577
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 387
2X-RAY DIFFRACTION1A388 - 390
3X-RAY DIFFRACTION1A391 - 1492
4X-RAY DIFFRACTION2B7 - 387
5X-RAY DIFFRACTION2B388
6X-RAY DIFFRACTION2B389 - 1491

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