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- PDB-1vq1: Crystal structure of N5-glutamine methyltransferase, HemK(EC 2.1.... -

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Basic information

Entry
Database: PDB / ID: 1vq1
TitleCrystal structure of N5-glutamine methyltransferase, HemK(EC 2.1.1.-) (TM0488) from Thermotoga maritima at 2.80 A resolution
ComponentsN5-glutamine methyltransferase, HemK
KeywordsTRANSFERASE / TM0488 / N5-glutamine methyltransferase / HEMK(EC 2.1.1.-) / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


peptide chain release factor N5-glutamine methyltransferase / protein-(glutamine-N5) methyltransferase activity / macromolecule modification / protein-glutamine N-methyltransferase activity / protein metabolic process / methylation / nucleic acid binding
Similarity search - Function
Methyltransferase HemK-like / Protein-(glutamine-N5) methyltransferase, release factor-specific / Release factor glutamine methyltransferase, N-terminal domain / PrmC N-terminal domain / Methyltransferase small domain / Methyltransferase small domain / DNA methylase, N-6 adenine-specific, conserved site / Ubiquitin-associated (UBA) domain / Helicase, Ruva Protein; domain 3 / Vaccinia Virus protein VP39 ...Methyltransferase HemK-like / Protein-(glutamine-N5) methyltransferase, release factor-specific / Release factor glutamine methyltransferase, N-terminal domain / PrmC N-terminal domain / Methyltransferase small domain / Methyltransferase small domain / DNA methylase, N-6 adenine-specific, conserved site / Ubiquitin-associated (UBA) domain / Helicase, Ruva Protein; domain 3 / Vaccinia Virus protein VP39 / 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 / Release factor glutamine methyltransferase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of N5-glutamine methyltransferase, HemK(EC 2.1.1.-) (TM0488) from Thermotoga maritima at 2.80 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionDec 2, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2005Provider: 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 / 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
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N5-glutamine methyltransferase, HemK
B: N5-glutamine methyltransferase, HemK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,4964
Polymers66,6992
Non-polymers7972
Water1267
1
A: N5-glutamine methyltransferase, HemK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7482
Polymers33,3501
Non-polymers3981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: N5-glutamine methyltransferase, HemK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7482
Polymers33,3501
Non-polymers3981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)140.973, 58.611, 85.667
Angle α, β, γ (deg.)90.00, 109.46, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:

Component-ID: 1 / Refine code: 2

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGGLUGLUAA12 - 8524 - 97
21ARGARGGLUGLUBB12 - 8524 - 97
12LYSLYSSERSERAA86 - 28298 - 294
22LYSLYSSERSERBB86 - 28298 - 294

NCS ensembles :
ID
1
2

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Components

#1: Protein N5-glutamine methyltransferase, HemK


Mass: 33349.504 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: TM0488 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9WYV8, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.85 Å3/Da / Density % sol: 56.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 7.5
Details: 5.0% MPD, 10.0% PEG-6000, 0.1M HEPES pH 7.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9796
DetectorType: ADSC / Detector: CCD / Date: Dec 13, 2003
RadiationMonochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.8→36.09 Å / Num. obs: 15828 / % possible obs: 96 % / Redundancy: 3.4 % / Biso Wilson estimate: 74.56 Å2 / Rsym value: 0.064 / Net I/σ(I): 13.3
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 1.7 / Num. unique all: 884 / Rsym value: 0.463 / % possible all: 73.3

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA4.2)data scaling
MOLREPphasing
REFMAC5.2.0005refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1nv8

1nv8


Resolution: 2.8→36.09 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.901 / SU B: 42.973 / SU ML: 0.375 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.416 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DUE TO LACK OF DENSITY, THE FOLLOWING REGIONS WERE NOT MODELED: A/B1-11, A207-211, B205-211. SAM MODELED BASED ON RELATED STRUCTURE (1NV8)
RfactorNum. reflection% reflectionSelection details
Rfree0.27281 801 5.1 %RANDOM
Rwork0.20824 ---
obs0.21156 15024 95.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 85.35 Å2
Baniso -1Baniso -2Baniso -3
1-5.5 Å20 Å2-1.54 Å2
2---7.5 Å20 Å2
3---0.98 Å2
Refinement stepCycle: LAST / Resolution: 2.8→36.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4116 0 54 7 4177
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224246
X-RAY DIFFRACTIONr_bond_other_d0.0020.024005
X-RAY DIFFRACTIONr_angle_refined_deg1.5072.0025728
X-RAY DIFFRACTIONr_angle_other_deg0.7839256
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1975526
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.81723.146178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.37515744
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.091533
X-RAY DIFFRACTIONr_chiral_restr0.0710.2654
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024658
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02891
X-RAY DIFFRACTIONr_nbd_refined0.230.2988
X-RAY DIFFRACTIONr_nbd_other0.1940.24203
X-RAY DIFFRACTIONr_nbtor_other0.0890.22605
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.2105
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2320.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.220.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3520.21
X-RAY DIFFRACTIONr_mcbond_it0.99532689
X-RAY DIFFRACTIONr_mcbond_other0.38331094
X-RAY DIFFRACTIONr_mcangle_it1.39454219
X-RAY DIFFRACTIONr_scbond_it3.28581736
X-RAY DIFFRACTIONr_scangle_it4.495111509
X-RAY DIFFRACTIONr_nbtor_refined0.1930.22117
Refine LS restraints NCS

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

Ens-IDNumberTypeRms dev position (Å)Weight position
1435tight positional0.030.05
1688medium positional0.310.5
1435tight thermal0.110.5
1688medium thermal0.582
21117tight positional0.040.05
21749medium positional0.360.5
21117tight thermal0.140.5
21749medium thermal0.762
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 53 6.02 %
Rwork0.346 827 -
obs--72.79 %
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)
16.08320.1555-2.397111.42571.80029.74910.52640.450.3394-0.6257-0.1156-0.20670.0728-0.1706-0.4109-0.04910.0373-0.2921-0.01240.1524-0.28416.988111.95539.8928
23.90330.17221.43965.8365-1.33028.00990.1494-0.2047-0.05980.10870.26990.72380.1546-1.1116-0.4193-0.4297-0.0136-0.0507-0.34340.0767-0.308510.1764-3.23938.6992
312.3897-4.5672.997728.30962.618129.82290.805-0.54031.24761.317-1.28410.1522-2.4636-1.7830.47910.1358-0.07280.2074-0.07520.13880.20465.4521-28.085615.6415
45.78760.3821-0.88628.9155-1.32775.2313-0.16320.73470.2623-0.06450.53231.21550.0553-0.5838-0.369-0.3091-0.00060.0578-0.35990.0997-0.085826.104-13.4976-5.3668
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA12 - 8524 - 97
22AA86 - 28298 - 294
33BB12 - 8524 - 97
44BB86 - 28298 - 294

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