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- PDB-4ava: Crystal structure of protein lysine acetyltransferase Rv0998 from... -

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Basic information

Entry
Database: PDB / ID: 4ava
TitleCrystal structure of protein lysine acetyltransferase Rv0998 from Mycobacterium tuberculosis
ComponentsLYSINE ACETYLTRANSFERASE
KeywordsTRANSFERASE / ALLOSTERIC REGULATION / DOMAIN COUPLING
Function / homology
Function and homology information


acyltransferase activity / acetyltransferase activity / cAMP binding / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / DNA-binding transcription factor activity / metal ion binding / cytosol
Similarity search - Function
Acetyltransferase (GNAT) domain / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding, conserved site / Gcn5-related N-acetyltransferase (GNAT) / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Gcn5-related N-acetyltransferase (GNAT) domain profile. ...Acetyltransferase (GNAT) domain / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding, conserved site / Gcn5-related N-acetyltransferase (GNAT) / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Jelly Rolls / Acyl-CoA N-acyltransferase / Aminopeptidase / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETYL COENZYME *A / ACETATE ION / DI(HYDROXYETHYL)ETHER / Acetyltransferase Pat
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.698 Å
AuthorsLee, H.J. / Lang, P.T. / Fortune, S.M. / Sassetti, C.M. / Alber, T.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Cyclic AMP Regulation of Protein Lysine Acetylation in Mycobacterium Tuberculosis.
Authors: Lee, H.J. / Lang, P.T. / Fortune, S.M. / Sassetti, C.M. / Alber, T.
History
DepositionMay 24, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LYSINE ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,01510
Polymers35,6621
Non-polymers1,3539
Water4,360242
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.418, 65.447, 77.761
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein LYSINE ACETYLTRANSFERASE


Mass: 35661.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O05581

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Non-polymers , 6 types, 251 molecules

#2: Chemical ChemComp-ACO / ACETYL COENZYME *A / Acetyl-CoA


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 2.09 Å3/Da / Density % sol: 41.1 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Details: DOUBLE CRYSTAL SI(111)
RadiationMonochromator: DOUBLE FLAT CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 1.7→45 Å / Num. obs: 34752 / % possible obs: 98.4 % / Observed criterion σ(I): 1.5 / Redundancy: 3.9 % / Biso Wilson estimate: 28.31 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 30
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 1.6 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.698→44.786 Å / SU ML: 0.45 / σ(F): 1.33 / Phase error: 24.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2296 1742 5 %
Rwork0.1908 --
obs0.1927 34696 98.3 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.098 Å2 / ksol: 0.345 e/Å3
Displacement parametersBiso mean: 39.5 Å2
Baniso -1Baniso -2Baniso -3
1-11.9229 Å20 Å20 Å2
2---5.2068 Å20 Å2
3----6.7162 Å2
Refinement stepCycle: LAST / Resolution: 1.698→44.786 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2457 0 86 242 2785
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012620
X-RAY DIFFRACTIONf_angle_d1.4113559
X-RAY DIFFRACTIONf_dihedral_angle_d13.445971
X-RAY DIFFRACTIONf_chiral_restr0.105408
X-RAY DIFFRACTIONf_plane_restr0.007462
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6978-1.74780.38071170.35542708X-RAY DIFFRACTION98
1.7478-1.80420.34721380.29912754X-RAY DIFFRACTION100
1.8042-1.86870.30061540.2522756X-RAY DIFFRACTION100
1.8687-1.94350.29231380.2322752X-RAY DIFFRACTION100
1.9435-2.03190.24111450.20712752X-RAY DIFFRACTION100
2.0319-2.13910.21991630.19642750X-RAY DIFFRACTION100
2.1391-2.27310.22161600.18742774X-RAY DIFFRACTION100
2.2731-2.44860.231550.18592764X-RAY DIFFRACTION100
2.4486-2.6950.24811330.18142796X-RAY DIFFRACTION99
2.695-3.08480.22041730.18962768X-RAY DIFFRACTION99
3.0848-3.88620.19281280.17322698X-RAY DIFFRACTION95
3.8862-44.80130.22561380.17612682X-RAY DIFFRACTION90
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)
11.42570.8685-0.921.2174-1.02471.7358-0.0768-0.1869-0.2998-0.1264-0.1733-0.13880.48130.21740.20950.4169-0.02040.12580.23920.00280.310445.158517.040141.4351
22.2721-0.16390.33231.6527-0.41031.60020.05691.0048-0.1558-0.4206-0.06330.1770.0587-0.3497-0.0010.2731-0.0006-0.0170.5601-0.05590.257638.078732.394128.1079
31.37580.3245-0.99211.4767-1.1062.95470.0976-0.18590.16810.20190.0165-0.0319-0.2490.1178-0.08270.21180.00120.02710.2579-0.00180.265152.28231.945235.8106
42.22971.4393-0.44882.6373-0.17170.29260.0936-0.4571-0.08170.4121-0.1999-0.0450.23540.18840.07950.2941-0.02040.01770.27080.01190.216955.892248.682828.2398
51.93370.7375-0.34891.9434-0.04290.89960.0563-0.21010.03240.2572-0.0117-0.06240.21370.0512-0.04320.27-0.0133-0.01710.23470.01420.214753.615145.140231.1978
62.38970.4716-0.15052.5592-0.08972.378-0.0069-0.16370.18980.2137-0.03050.1597-0.407-0.04330.03090.24080.0266-0.00160.1775-0.01340.22153.611262.907827.6051
72.8120.9192-1.2032.9855-1.88454.7934-0.0772-0.0397-0.0595-0.49780.29150.56550.567-0.3799-0.29130.2253-0.0087-0.08320.29730.02560.314244.878648.08117.8891
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 2:41)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 42:114)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 115:140)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 141:192)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 193:216)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 217:314)
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 315:333)

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