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- PDB-3fnc: Crystal structure of a putative acetyltransferase from Listeria i... -

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Basic information

Entry
Database: PDB / ID: 3fnc
TitleCrystal structure of a putative acetyltransferase from Listeria innocua
ComponentsPutative acetyltransferase
KeywordsTRANSFERASE / GNAT / RimI / Acetyltransferase / Listeria innocua / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function
: / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
MALONATE ION / Lin0611 protein
Similarity search - Component
Biological speciesListeria innocua (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å
AuthorsCuff, M.E. / Tesar, C. / Freeman, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: The structure of a putative acetyltransferase from Listeria innocua.
Authors: Cuff, M.E. / Tesar, C. / Freeman, L. / Joachimiak, A.
History
DepositionDec 24, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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: Putative acetyltransferase
B: Putative acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,55814
Polymers37,6932
Non-polymers86512
Water5,765320
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.974, 61.030, 75.132
Angle α, β, γ (deg.)90.000, 92.080, 90.000
Int Tables number4
Space group name H-MP1211
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

#1: Protein Putative acetyltransferase / Protein Lin0611


Mass: 18846.701 Da / Num. of mol.: 2 / Fragment: UNP residues 1-160
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria innocua (bacteria) / Strain: Clip11262 / Gene: lin0611 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q92E50
#2: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H2O4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.43 Å3/Da / Density % sol: 49.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.4M Na Malonate, DMSO, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97962, 0.97945
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Jul 30, 2008
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979621
20.979451
ReflectionRedundancy: 4.3 % / Av σ(I) over netI: 27.53 / Number: 154593 / Rmerge(I) obs: 0.073 / Χ2: 1.64 / D res high: 1.75 Å / D res low: 50 Å / Num. obs: 35751 / % possible obs: 97.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.755097.110.0685.3484.2
3.774.7598.810.0583.3373.9
3.293.7799.610.0632.9124.4
2.993.2999.710.0662.3414.4
2.782.9999.710.0732.0414.5
2.612.7899.910.0731.6274.6
2.482.6110010.0761.4794.6
2.382.4899.910.0831.3814.6
2.282.3810010.0851.2274.6
2.22.2810010.0871.1674.6
2.142.210010.0941.144.6
2.072.1410010.1021.1174.6
2.022.0710010.1111.1124.6
1.972.0210010.1191.0054.6
1.931.9710010.1420.9794.7
1.891.9310010.1690.9624.6
1.851.8999.210.1830.8724
1.811.8592.910.2130.8313.5
1.781.8185.210.2310.7833.4
1.751.7881.110.2680.7793.2
ReflectionResolution: 1.75→50 Å / Num. all: 35751 / Num. obs: 35751 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.073 / Χ2: 1.644 / Net I/σ(I): 27.534
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.268 / Num. unique all: 1464 / Χ2: 0.779 / % possible all: 81.1

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Phasing

PhasingMethod: MAD
Phasing MADD res high: 1.75 Å / D res low: 50 Å / FOM : 0.305 / FOM acentric: 0.312 / FOM centric: 0.122 / Reflection: 35702 / Reflection acentric: 34253 / Reflection centric: 1449
Phasing MAD set

Highest resolution: 1.75 Å / Lowest resolution: 50 Å

IDR cullis acentricR cullis centricLoc acentricLoc centricPower acentricPower centricReflection acentricReflection centric
11.6210.10.100342531449
20.970.945.67.80.370.31325041043
Phasing MAD set shell
IDResolution (Å)R cullis acentricR cullis centricLoc acentricLoc centricPower acentricPower centricReflection acentricReflection centric
111.24-503.310.60.10010728
16.33-11.241.5510.30.20056979
14.41-6.331.2110.20.2001388115
13.38-4.411.0810.20.1002640154
12.74-3.381.3710.10.1004248206
12.31-2.741.7910.10006194260
11.99-2.312.56100008535302
11.75-1.99111000010572305
211.24-500.840.86.56.81.781.299515
26.33-11.240.810.736.57.41.260.9152346
24.41-6.330.940.948.68.80.680.55122376
23.38-4.410.950.888.812.90.540.37247894
22.74-3.380.950.9268.40.550.434059133
22.31-2.740.980.9657.10.40.265962187
21.99-2.310.990.994.86.70.260.178273233
21.75-1.99115.370.140.19891259
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se22.605240.0630.0620.3910
2Se30.727750.1480.0630.4240
3Se30.86727-0.407-0.0560.1020
4Se27.83745-0.319-0.0570.0770
5Se31.14576-0.822-0.1690.0190
6Se41.08445-0.3320.1830.4750
7Se22.721720.0610.0630.391-0.106
8Se29.989520.1470.0630.424-0.125
9Se27.92736-0.405-0.0560.102-0.105
10Se26.86262-0.318-0.0570.077-0.106
11Se31.46373-0.82-0.170.019-0.07
12Se35.65702-0.3320.1830.476-0.048
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
11.24-500.6240.7170.26813510728
6.33-11.240.6210.6690.2764856979
4.41-6.330.4760.5010.1815031388115
3.38-4.410.460.4760.19127942640154
2.74-3.380.4770.4920.1744544248206
2.31-2.740.3820.3920.12164546194260
1.99-2.310.2660.2730.06688378535302
1.75-1.990.1330.1360.0361087710572305
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 35702
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
7.26-10058.60.803514
5.77-7.2650.60.878513
4.93-5.7756.90.885627
4.37-4.9360.90.891689
3.97-4.3759.10.891790
3.66-3.9751.50.907859
3.42-3.6654.40.882941
3.21-3.42530.892985
3.04-3.21530.8951031
2.9-3.0453.10.8811101
2.77-2.952.60.8771160
2.66-2.7754.40.8811190
2.56-2.6652.20.8981271
2.47-2.5654.90.8791292
2.39-2.4757.20.8821339
2.32-2.3959.50.8721399
2.25-2.3258.10.8841406
2.19-2.2563.40.8711474
2.14-2.1961.90.8751486
2.08-2.1464.50.8761530
2.04-2.0863.90.8761590
1.99-2.0466.40.8791615
1.95-1.9968.20.8691666
1.91-1.9569.80.8571668
1.87-1.9173.30.8381722
1.84-1.8776.60.8261725
1.8-1.8478.70.8031587
1.75-1.879.40.7482532

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DM6phasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building
RefinementMethod to determine structure: MAD / Resolution: 1.75→28.27 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.204 / WRfactor Rwork: 0.177 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.904 / SU B: 4.516 / SU ML: 0.067 / SU R Cruickshank DPI: 0.116 / SU Rfree: 0.108 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.114 / ESU R Free: 0.109
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.201 1781 5 %RANDOM
Rwork0.169 ---
all0.17 35701 --
obs0.17 35701 97.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 58.53 Å2 / Biso mean: 18.526 Å2 / Biso min: 4.39 Å2
Baniso -1Baniso -2Baniso -3
1--0.86 Å20 Å20.13 Å2
2--0.11 Å20 Å2
3---0.76 Å2
Refinement stepCycle: LAST / Resolution: 1.75→28.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2615 0 57 320 2992
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222812
X-RAY DIFFRACTIONr_angle_refined_deg1.341.9443806
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.845336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.86724.483145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.41315456
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1091511
X-RAY DIFFRACTIONr_chiral_restr0.0950.2410
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212195
X-RAY DIFFRACTIONr_mcbond_it0.8071.51654
X-RAY DIFFRACTIONr_mcangle_it1.50522691
X-RAY DIFFRACTIONr_scbond_it2.41731158
X-RAY DIFFRACTIONr_scangle_it4.0344.51115
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 111 -
Rwork0.213 2097 -
all-2208 -
obs--81.78 %
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)
11.40070.0555-0.27681.35010.27141.11610.06530.1604-0.0588-0.0416-0.0604-0.0126-0.007-0.0766-0.00490.02020.0023-0.00360.0291-0.00820.00520.536225.326646.1231
22.0035-0.25080.17330.9895-0.11250.54360.0566-0.19440.03340.0067-0.05510.04570.0255-0.023-0.00150.0357-0.00660.0030.0384-0.01620.009418.608236.044966.4528
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-3 - 160
2X-RAY DIFFRACTION2B-3 - 160

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