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- PDB-1vlm: Crystal structure of SAM-dependent methyltransferase, possible hi... -

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Basic information

Entry
Database: PDB / ID: 1vlm
TitleCrystal structure of SAM-dependent methyltransferase, possible histamine N-methyltransferase (TM1293) from Thermotoga maritima at 2.20 A resolution
ComponentsSAM-dependent methyltransferase
KeywordsTRANSFERASE / TM1293 / SAM-DEPENDENT METHYLTRANSFERASE / POSSIBLE HISTAMINE N-METHYLTRANSFERASE / STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI / Joint Center for Structural Genomics
Function / homologyMethyltransferase type 11 / Methyltransferase domain / methyltransferase activity / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Methyltransf_11 domain-containing protein
Function and homology information
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of SAM-dependent methyltransferase, possible histamine N-methyltransferase (TM1293) from Thermotoga maritima at 2.20 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 4, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_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: SAM-dependent methyltransferase
B: SAM-dependent methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4213
Polymers51,3982
Non-polymers231
Water1,964109
1
A: SAM-dependent methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7222
Polymers25,6991
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SAM-dependent methyltransferase


Theoretical massNumber of molelcules
Total (without water)25,6991
Polymers25,6991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.648, 70.734, 93.922
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: MSE / End label comp-ID: LYS / Refine code: 2 / Auth seq-ID: 1 - 207 / Label seq-ID: 13 - 219

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

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Components

#1: Protein SAM-dependent methyltransferase


Mass: 25698.844 Da / Num. of mol.: 2 / Mutation: 2.1.1.
Source method: isolated from a genetically manipulated source
Details: possible histamine N-methyltransferase / Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: TM1293 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X119
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.31 Å3/Da / Density % sol: 46.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop
Details: 20.00% NP_Isopropanol, 0.034M Na/K-Phosphate pH5.0, 0.066M Na/K-Phosphate pH 7.0, 5.00% Glycerol, 20.00% NP_PEG 4000 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
1,21
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONALS 8.2.111.0032
SYNCHROTRONALS 8.2.121.0032,0.9796,0.9794
DetectorType: ADSC / Detector: CCD / Date: Dec 12, 2003
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double Crystal Si(111)SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.00321
20.97961
30.97941
ReflectionResolution: 2.2→53.81 Å / Num. obs: 22405 / % possible obs: 98.4 % / Redundancy: 3.5 % / Biso Wilson estimate: 42.02 Å2 / Rsym value: 0.09 / Net I/σ(I): 9.9
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2 / Num. unique all: 1500 / Rsym value: 0.514 / % possible all: 92.1

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA4.2)data scaling
SHARPphasing
REFMAC5.2.0005refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.2→53.81 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.923 / SU B: 12.559 / SU ML: 0.16 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.279 / ESU R Free: 0.218
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. WEAK DENSITY FOR RESIDUES A140-149 3. SOME UNMODELED DENSITY NEAR A300 (NA ION)
RfactorNum. reflection% reflectionSelection details
Rfree0.2461 1148 5.1 %RANDOM
Rwork0.19162 ---
obs0.1943 21451 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.296 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å20 Å2
2---0.4 Å20 Å2
3---0.76 Å2
Refinement stepCycle: LAST / Resolution: 2.2→53.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3250 0 1 109 3360
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223335
X-RAY DIFFRACTIONr_bond_other_d0.0020.023110
X-RAY DIFFRACTIONr_angle_refined_deg1.4451.964495
X-RAY DIFFRACTIONr_angle_other_deg0.84637147
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6375412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.50222.55149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.56615566
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0561526
X-RAY DIFFRACTIONr_chiral_restr0.0850.2488
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023716
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02762
X-RAY DIFFRACTIONr_nbd_refined0.2080.2597
X-RAY DIFFRACTIONr_nbd_other0.1790.22988
X-RAY DIFFRACTIONr_nbtor_other0.0860.22113
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.297
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1190.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2430.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0790.23
X-RAY DIFFRACTIONr_mcbond_it1.65132050
X-RAY DIFFRACTIONr_mcbond_other0.4113852
X-RAY DIFFRACTIONr_mcangle_it2.9753279
X-RAY DIFFRACTIONr_scbond_it5.46981315
X-RAY DIFFRACTIONr_scangle_it7.898111215
X-RAY DIFFRACTIONr_nbtor_refined0.1850.21641
X-RAY DIFFRACTIONr_metal_ion_refined0.0890.21
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: B / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1209tight positional0.070.05
1864medium positional0.430.5
1209tight thermal0.210.5
1864medium thermal0.912
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 83 5.39 %
Rwork0.24 1458 -
obs--100 %
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)
12.50720.32760.33861.46360.83611.40040.015-0.0975-0.11240.00750.014-0.07720.10080.0987-0.0291-0.21640.008-0.0113-0.21160.0066-0.128750.20815.90686.816
23.6295-0.7872-2.71653.14250.20263.372-0.0087-0.05750.14580.040.03270.4096-0.2421-0.2535-0.0240.05210.0669-0.02560.004-0.0266-0.045654.10315.2236.555
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 1 - 206 / Label seq-ID: 13 - 218

IDRefine TLS-IDAuth asym-IDLabel asym-ID
11AA
22BB

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