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- PDB-2f8l: Crystal structure of a putative class i s-adenosylmethionine-depe... -

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Basic information

Entry
Database: PDB / ID: 2f8l
TitleCrystal structure of a putative class i s-adenosylmethionine-dependent methyltransferase (lmo1582) from listeria monocytogenes at 2.20 A resolution
Componentshypothetical protein lmo1582Hypothesis
KeywordsTRANSFERASE / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


N-methyltransferase activity / : / DNA binding
Similarity search - Function
DNA polymerase; domain 1 - #470 / S-adenosyl-L-methionine dependent adenine methyltransferase, bacteria, predicted / N-6 DNA Methylase / DNA methylase, adenine-specific / Vaccinia Virus protein VP39 / DNA polymerase; domain 1 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich ...DNA polymerase; domain 1 - #470 / S-adenosyl-L-methionine dependent adenine methyltransferase, bacteria, predicted / N-6 DNA Methylase / DNA methylase, adenine-specific / Vaccinia Virus protein VP39 / DNA polymerase; domain 1 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / : / Lmo1582 protein
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of (16411011) from Listeria monocytogenes LI2 at 2.20 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionDec 2, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A MONOMER AS A BIOLOGICALLY SIGNIFICANT OLIGIMERIZATION STATE.
Remark 999SEQUENCE THE STRAIN CLONED DIFFERS FROM THE SEQUENCED STRAIN IN THE DATABASE. DNA SEQUENCING ...SEQUENCE THE STRAIN CLONED DIFFERS FROM THE SEQUENCED STRAIN IN THE DATABASE. DNA SEQUENCING CONFIRMED THE FOLLOWING STRAIN VARIATIONS - E60A, I120V, R291E, and N296D. THE ELECTRON DENSITY SUPPORTS THESE ASSIGNMENTS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein lmo1582
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9409
Polymers38,9491
Non-polymers9908
Water2,774154
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.595, 99.595, 117.084
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
DetailsSIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A MONOMER AS A BIOLOGICALLY SIGNIFICANT OLIGIMERIZATION STATE.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein hypothetical protein lmo1582 / Hypothesis


Mass: 38949.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: Li2 / Gene: 16411011 / Production host: Escherichia coli (E. coli) / References: GenBank: 16803622, UniProt: Q8Y6U9*PLUS

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Non-polymers , 5 types, 162 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 3.75 Å3/Da / Density % sol: 66.92 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 8
Details: 2.4M (NH4)2SO4, 0.1M TRIS, pH 8.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9797, 0.9796, 1.0000
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 28, 2005
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97971
20.97961
311
ReflectionResolution: 2.2→23.65 Å / Num. obs: 28765 / % possible obs: 99.4 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 7.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsRsym value% possible all
2.2-2.2699.53.80.5821.221200.58299.5
2.26-2.3299.63.80.481.520570.48
2.32-2.3999.63.80.3741.920260.374
2.39-2.4699.73.80.3252.219670.325
2.46-2.5499.73.80.2632.719020.263
2.54-2.6399.73.80.2173.218430.217
2.63-2.7399.63.80.1714.117410.171
2.73-2.8499.53.80.139517210.139
2.84-2.9799.63.80.1155.816410.115
2.97-3.1199.53.70.097715600.097
3.11-3.2899.63.80.0758.915010.075
3.28-3.4899.43.70.06110.113910.061
3.48-3.7299.63.70.05211.113210.052
3.72-4.0299.43.70.04812.412340.048
4.02-4.499.53.70.04712.511430.047
4.4-4.9299.23.70.04413.710250.044
4.92-5.6899.43.60.04713.29000.047
5.68-6.9699.13.50.05112.67700.051
6.96-9.8498.93.40.04413.45980.044
9.84-23.6591.13.20.04114.53040.041

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
SCALAdata scaling
PDB_EXTRACT1.601data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→23.66 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.946 / SU B: 7.047 / SU ML: 0.095 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.15
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.211 1463 5.1 %RANDOM
Rwork0.165 ---
all0.168 ---
obs0.16769 27324 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.117 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å20 Å20 Å2
2--0.83 Å20 Å2
3----1.66 Å2
Refinement stepCycle: LAST / Resolution: 2.2→23.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2518 0 63 154 2735
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222652
X-RAY DIFFRACTIONr_bond_other_d0.0010.021760
X-RAY DIFFRACTIONr_angle_refined_deg1.5852.0023588
X-RAY DIFFRACTIONr_angle_other_deg0.99134356
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6735326
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.53226.293116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.48815474
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.051156
X-RAY DIFFRACTIONr_chiral_restr0.0920.2418
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022876
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02464
X-RAY DIFFRACTIONr_nbd_refined0.2020.2535
X-RAY DIFFRACTIONr_nbd_other0.1910.21823
X-RAY DIFFRACTIONr_nbtor_refined0.1720.21279
X-RAY DIFFRACTIONr_nbtor_other0.0860.21356
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2156
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.040.23
X-RAY DIFFRACTIONr_symmetry_vdw_other0.150.222
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.214
X-RAY DIFFRACTIONr_mcbond_it2.01231685
X-RAY DIFFRACTIONr_mcbond_other0.5273659
X-RAY DIFFRACTIONr_mcangle_it3.03752633
X-RAY DIFFRACTIONr_scbond_it5.35581089
X-RAY DIFFRACTIONr_scangle_it6.94611955
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 107 -
Rwork0.233 2013 -
obs--99.48 %
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)
16.15181.6250.17432.8822-1.32855.027-0.0315-1.44140.0311.0116-0.2292-0.823-0.54290.82310.26070.2246-0.0779-0.34230.4869-0.0020.178254.995520.841160.3799
21.595-0.9590.07763.20320.14372.0716-0.0323-0.06010.04180.12910.0853-0.2219-0.07850.1303-0.053-0.2008-0.03550.0044-0.20120.0072-0.207338.919718.234437.0058
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: all / Auth asym-ID: A

IDRefine TLS-IDLabel asym-IDAuth seq-IDLabel seq-ID
11A2 - 9114 - 103
22A - D92 - 400104 - 1

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