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- PDB-4ijn: Crystal structure of an acetate kinase from Mycobacterium smegmat... -

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Basic information

Entry
Database: PDB / ID: 4ijn
TitleCrystal structure of an acetate kinase from Mycobacterium smegmatis bound to AMP and sulfate
ComponentsAcetate kinase
KeywordsTRANSFERASE / proprionate kinase / ATP-dependent / Metabolic intermediate biosynthesis / acetyl-CoA biosynthesis / hydrolysis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


acetate kinase / acetate kinase activity / acetate metabolic process / 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
ADENOSINE MONOPHOSPHATE / Acetate kinase
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 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
DepositionDec 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.3Sep 20, 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_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: Acetate kinase
B: Acetate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,1779
Polymers85,1052
Non-polymers1,0737
Water12,556697
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8580 Å2
ΔGint-90 kcal/mol
Surface area27140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.430, 81.910, 95.400
Angle α, β, γ (deg.)90.000, 96.510, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Acetate kinase / Acetokinase


Mass: 42552.336 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Gene: ackA, MSMEG_0784, MSMEI_0768 / Plasmid: pAVA0421 / Production host: Escherichia coli (E. coli) / References: UniProt: A0QQK1, acetate kinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 697 / 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: 2.53 Å3/Da / Density % sol: 51.35 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: MysmA.00640.a.A1 PS00601 at 20 mg/mL with 2 mM AMP and 2 mM MnCl2 against JCSG+ condition H7, 25% PEG 3350, 0.1 M BisTris, 0.2 M ammonium sulfate with 15% ethylene glycol as cryo-protectant, ...Details: MysmA.00640.a.A1 PS00601 at 20 mg/mL with 2 mM AMP and 2 mM MnCl2 against JCSG+ condition H7, 25% PEG 3350, 0.1 M BisTris, 0.2 M ammonium sulfate with 15% ethylene glycol as cryo-protectant, crystal tracking ID 238414h7, unique puck ID gpy2-6, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Nov 24, 2012 / Details: VariMax
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 93194 / Num. obs: 91223 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 23.913 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 20.66
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.7-1.740.293.2213326622090.2
1.74-1.790.2584.2718558621593
1.79-1.840.2164.9719058617695
1.84-1.90.1855.8119435612196.7
1.9-1.960.1427.519511599498.1
1.96-2.030.1119.3820013589799.2
2.03-2.110.09311.8420133571299.6
2.11-2.190.07915.37231645480100
2.19-2.290.0719.2124834529999.7
2.29-2.40.06321.4225032506199.8
2.4-2.530.05923.7425151478899.9
2.53-2.690.05327.9225326451399.4
2.69-2.870.04832.5228180427699.9
2.87-3.10.04537.4229308400799.8
3.1-3.40.0442.9226737368099.9
3.4-3.80.03549.1423658331599.7
3.8-4.390.03353.0520880292499.7
4.39-5.380.03154.9217998249599.6
5.38-7.60.03252.88142341959100
7.60.0358.657549109198.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å45.7 Å
Translation3 Å45.7 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.2phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
StructureStudiodata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3r9p

3r9p


Resolution: 1.7→45.74 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.1954 / WRfactor Rwork: 0.1677 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8981 / SU B: 3.459 / SU ML: 0.06 / SU R Cruickshank DPI: 0.0976 / SU Rfree: 0.0953 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.098 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES WITH TLS ADDED. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2015 4566 5 %RANDOM
Rwork0.1733 ---
obs0.1747 91201 97.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 52.05 Å2 / Biso mean: 19.5464 Å2 / Biso min: 7.13 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å2-0 Å2-0.67 Å2
2--0.43 Å20 Å2
3---0.44 Å2
Refinement stepCycle: LAST / Resolution: 1.7→45.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5570 0 68 697 6335
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195810
X-RAY DIFFRACTIONr_bond_other_d0.0010.025554
X-RAY DIFFRACTIONr_angle_refined_deg1.4841.9847933
X-RAY DIFFRACTIONr_angle_other_deg0.775312748
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4145771
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.39622.987231
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.90615889
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3011546
X-RAY DIFFRACTIONr_chiral_restr0.0840.2926
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216621
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021271
X-RAY DIFFRACTIONr_mcbond_it0.7771.1123026
X-RAY DIFFRACTIONr_mcbond_other0.7761.1113025
X-RAY DIFFRACTIONr_mcangle_it1.2751.6643785
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 328 -
Rwork0.219 5886 -
all-6214 -
obs--90.24 %
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)
10.2978-0.12730.08660.108-0.10770.3681-0.0338-0.00280.01660.0641-0.002-0.027-0.0163-0.00080.03580.0747-0.0008-0.01120.00320.00120.075157.49545.03450.7428
20.4237-0.05960.19330.0441-0.07630.4470.0460.186-0.02310.0268-0.03790.00520.0058-0.008-0.00810.04460.00830.00320.1277-0.0110.033942.28314.2728-32.3144
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 376
2X-RAY DIFFRACTION2B2 - 376

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