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- PDB-3p4i: Crystal structure of acetate kinase from Mycobacterium avium -

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Basic information

Entry
Database: PDB / ID: 3p4i
TitleCrystal structure of acetate kinase from Mycobacterium avium
ComponentsAcetate kinase
KeywordsTRANSFERASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / mycobacterium / tuberculosis / non-pathogenic species / ortholog / pyruvate / propanoate / acetyl-CoA biosynthesis / kinase
Function / homology
Function and homology information


acetate kinase / organic acid metabolic process / acetate kinase activity / acetyl-CoA biosynthetic process / phosphorylation / 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
Biological speciesMycobacterium avium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 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
DepositionOct 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2010Provider: 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 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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: Acetate kinase
B: Acetate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,3643
Polymers83,3022
Non-polymers621
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6340 Å2
ΔGint-47 kcal/mol
Surface area30840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.640, 101.710, 105.770
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 6 / Auth seq-ID: 8 - 385 / Label seq-ID: 12 - 389

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Acetate kinase /


Mass: 41651.051 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium avium (bacteria) / Gene: ackA, MAV_4758 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / References: UniProt: A0QLU8, acetate kinase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.76 Å3/Da / Density % sol: 55.51 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: protein at 23.4 mg/mL, 10 % PEG 8000, 0.1 M Tris pH 7.0, 0.1 M MgCl2 with 25% ethylene glycol as cryo-protectant, crsytal tracking ID 216702h7, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 28, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. all: 39172 / Num. obs: 39051 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 42.778 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 12.15
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.35-2.410.5313.4158372840100
2.41-2.480.4953.7155872795100
2.48-2.550.4174.2151192714100
2.55-2.630.3784.714604262499.9
2.63-2.710.3025.8143082573100
2.71-2.810.2516.813564244099.8
2.81-2.910.227.7132752393100
2.91-3.030.1898.812757230299.9
3.03-3.170.15210.5122782231100
3.17-3.320.11613.511548212399.9
3.32-3.50.09615.610890201299.8
3.5-3.720.0818.610164189599.3
3.72-3.970.0720.79381179999.7
3.97-4.290.06122.58777168599.5
4.29-4.70.055247810155799.3
4.7-5.250.0524.97237139598.8
5.25-6.070.05124.36767126199.4
6.07-7.430.051245716107399.2
7.43-10.510.0428.6433785198.7
10.510.03729.3228148896.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 59.18 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å39.69 Å
Translation3 Å39.69 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 1tuy

1tuy


Resolution: 2.35→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.927 / WRfactor Rfree: 0.2174 / WRfactor Rwork: 0.1723 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.847 / SU B: 14.91 / SU ML: 0.157 / SU R Cruickshank DPI: 0.2897 / SU Rfree: 0.2198 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2298 1946 5 %RANDOM
Rwork0.1823 ---
obs0.1847 38908 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 128.73 Å2 / Biso mean: 37.2275 Å2 / Biso min: 14.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.49 Å20 Å20 Å2
2--2.82 Å20 Å2
3----1.33 Å2
Refinement stepCycle: LAST / Resolution: 2.35→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5633 0 4 232 5869
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0215763
X-RAY DIFFRACTIONr_angle_refined_deg1.4721.9667841
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7545765
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.77822.49245
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.90415883
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6631558
X-RAY DIFFRACTIONr_chiral_restr0.0940.2912
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214424
X-RAY DIFFRACTIONr_mcbond_it0.6141.53766
X-RAY DIFFRACTIONr_mcangle_it1.16126008
X-RAY DIFFRACTIONr_scbond_it1.85431997
X-RAY DIFFRACTIONr_scangle_it3.1464.51829
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2739 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
LOOSE POSITIONAL0.425
LOOSE THERMAL3.0510
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 147 -
Rwork0.228 2680 -
all-2827 -
obs--99.82 %
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)
11.43240.49310.090.84720.47230.30370.0073-0.15510.1291-0.1017-0.04480.0676-0.0438-0.02050.03750.1329-0.0254-0.05190.14410.02410.183728.062848.016515.0253
20.08470.05970.05240.2362-0.07790.1052-0.05970.00450.0311-0.01930.07960.0568-0.0492-0.0262-0.01980.1615-0.0063-0.01530.18130.03490.172826.39527.235716.5519
32.3204-1.2238-0.6231.31110.5870.30360.0333-0.05190.12820.04850.0469-0.1212-0.07880.0357-0.08020.2741-0.04460.02390.1585-0.03150.123739.16928.172238.4162
40.13530.0878-0.07130.2174-0.0410.209-0.025-0.01740.004-0.02090.0615-0.00930.01150.0327-0.03650.1623-0.0129-0.00730.17950.00310.156943.725522.850717.7082
52.4266-0.7393-0.63321.02210.61130.4914-0.10810.37930.007-0.006-0.02060.01220.064-0.17010.12870.0764-0.11060.0330.2887-0.07850.1686.1974-13.101235.5937
614.6013-3.8332-5.86241.0221.53182.3572-1.62382.8153-4.13850.5831-0.38331.04480.7484-1.14352.00710.5931-0.2440.35680.6069-0.87351.28832.7156-21.87937.1931
70.65140.7561-0.58521.2113-0.46090.743-0.01380.10340.03330.0456-0.0082-0.01330.0224-0.16180.0220.1408-0.02450.00390.20810.02180.134413.6391-3.903945.2961
80.056-0.024-0.07070.2473-0.14920.2317-0.01330.00930.01180.00770.0520.00880.0405-0.0452-0.03870.147-0.0236-0.01910.20060.02650.146124.78962.195823.2796
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 122
2X-RAY DIFFRACTION2A123 - 259
3X-RAY DIFFRACTION3A260 - 285
4X-RAY DIFFRACTION4A286 - 388
5X-RAY DIFFRACTION5B8 - 57
6X-RAY DIFFRACTION6B58 - 71
7X-RAY DIFFRACTION7B72 - 138
8X-RAY DIFFRACTION8B139 - 388

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