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- PDB-4dq8: Crystal structure of acetate kinase AckA from Mycobacterium marinum -

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Basic information

Entry
Database: PDB / ID: 4dq8
TitleCrystal structure of acetate kinase AckA from Mycobacterium marinum
ComponentsAcetate kinase
KeywordsTRANSFERASE / acetokinase / mycobacterium / ATP-dependent / metabolic intermediate biosynthesis / acetyl-CoA biosynthesis / cytoplasmic / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
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 and butyrate kinases family signature 2. / 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
Biological speciesMycobacterium marinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 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
DepositionFeb 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acetate kinase
B: Acetate kinase


Theoretical massNumber of molelcules
Total (without water)83,7332
Polymers83,7332
Non-polymers00
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6310 Å2
ΔGint-41 kcal/mol
Surface area27740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.500, 87.170, 176.740
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Acetate kinase / Acetokinase


Mass: 41866.445 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium marinum (bacteria) / Strain: ATCC BAA-535 / M / Gene: ackA, MMAR_0711 / Plasmid: pAVA0421 / Production host: Escherichia coli (E. coli) / References: UniProt: B2HPZ3, acetate kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 2.55 Å3/Da / Density % sol: 51.82 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: MymaA.00640.a.A1 PW29994 at 14.2 mg/mL against PACT C10 focus screen, 0.2 M MgCl2, 0.1 M Hepes, 18% PEG 6000 with 20% ethylene glycol as cryo-protectant, crystal tracking ID 220845f4, pH 7. ...Details: MymaA.00640.a.A1 PW29994 at 14.2 mg/mL against PACT C10 focus screen, 0.2 M MgCl2, 0.1 M Hepes, 18% PEG 6000 with 20% ethylene glycol as cryo-protectant, crystal tracking ID 220845f4, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 25, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. all: 41660 / Num. obs: 41517 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 48.334 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 18.99
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.25-2.310.4633.2315549300899.4
2.31-2.370.3724.1615465290999.4
2.37-2.440.3634.3715685288299.7
2.44-2.520.285.7715767281899.9
2.52-2.60.2317.1715261267799.9
2.6-2.690.1789.2115164261799.9
2.69-2.790.15111.0814981254699.7
2.79-2.90.11714.23146142465100
2.9-3.030.116.813807234299.9
3.03-3.180.07820.7712968223099.9
3.18-3.350.06624.5712386216499.8
3.35-3.560.05229.8811408201899.9
3.56-3.80.04534.6310767192499.6
3.8-4.110.043710131180799.9
4.11-4.50.03640.279361164899.6
4.5-5.030.03142.288707151899.7
5.03-5.810.02941.167748134799.9
5.81-7.120.02541.4167441159100
7.12-10.060.01945.33525191799.7
10.060.01944.36269152192

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 46.57 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å19.99 Å
Translation3.5 Å19.99 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3p4i

3p4i


Resolution: 2.25→42.32 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.912 / WRfactor Rfree: 0.2512 / WRfactor Rwork: 0.206 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8481 / SU B: 12.607 / SU ML: 0.161 / SU R Cruickshank DPI: 0.2774 / SU Rfree: 0.225 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.277 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES WITH TLS ADDED. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2601 2099 5.1 %RANDOM
Rwork0.2106 ---
obs0.2131 41316 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 104.03 Å2 / Biso mean: 48.3121 Å2 / Biso min: 19.34 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20 Å2
2--0.11 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.25→42.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5385 0 0 190 5575
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195492
X-RAY DIFFRACTIONr_bond_other_d0.0010.023540
X-RAY DIFFRACTIONr_angle_refined_deg1.3181.9657487
X-RAY DIFFRACTIONr_angle_other_deg0.9338615
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.175739
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.82422.936218
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.40615775
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3341542
X-RAY DIFFRACTIONr_chiral_restr0.0710.2870
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216334
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021124
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 144 -
Rwork0.286 2631 -
all-2775 -
obs--98.93 %
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)
10.97050.13650.06351.2255-0.17710.39240.03410.4007-0.15340.02590.0560.10070.18010.0441-0.09010.13460.0850.02140.25490.01350.118-20.724-1.6116.5162
21.08540.3377-0.17820.67150.52250.88880.13550.18990.51080.09140.11240.1107-0.16560.0207-0.24790.17550.07340.16090.10160.12860.312-16.452831.488826.6904
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 386
2X-RAY DIFFRACTION2B7 - 385

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