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- PDB-2pxx: Human putative methyltransferase MGC2408 -

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Basic information

Entry
Database: PDB / ID: 2pxx
TitleHuman putative methyltransferase MGC2408
ComponentsUncharacterized protein MGC2408
KeywordsTRANSFERASE / Structural Genomics Consortium / SGC / methyltransferase / MGC2408 / LOC84291
Function / homology
Function and homology information


protein-lysine N-methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity
Similarity search - Function
Methyltransferase type 11 / Methyltransferase domain / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / EEF1A lysine methyltransferase 4 / EEF1A lysine methyltransferase 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / sad / Resolution: 1.3 Å
AuthorsTempel, W. / Wu, H. / Dombrovsky, L. / Zeng, H. / Zhu, H. / Loppnau, P. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. ...Tempel, W. / Wu, H. / Dombrovsky, L. / Zeng, H. / Zhu, H. / Loppnau, P. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Plotnikov, A.N. / Structural Genomics Consortium (SGC)
CitationJournal: Proteins / Year: 2009
Title: An intact SAM-dependent methyltransferase fold is encoded by the human endothelin-converting enzyme-2 gene.
Authors: Tempel, W. / Wu, H. / Dombrovsky, L. / Zeng, H. / Loppnau, P. / Zhu, H. / Plotnikov, A.N. / Bochkarev, A.
History
DepositionMay 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein MGC2408
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3013
Polymers23,9171
Non-polymers3842
Water2,432135
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.883, 45.560, 55.102
Angle α, β, γ (deg.)90.000, 105.870, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Uncharacterized protein MGC2408


Mass: 23916.855 Da / Num. of mol.: 1 / Fragment: Residues 19-231 / Mutation: R100C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MGC2408 / Plasmid: pET28a-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus RIL / References: UniProt: Q9BRZ8, UniProt: P0DPD7*PLUS
#2: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 1.8 Å3/Da / Density % sol: 32.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 5.5
Details: 28% PEG3350, 0.1 M Ammonium sulfate, 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 23-ID-D10.97926
SYNCHROTRONCHESS A120.9777
Detector
TypeIDDetectorDate
MARMOSAIC 300 mm CCD1CCDApr 16, 2007
ADSC QUANTUM 2102CCDMay 5, 2007
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979261
20.97771
ReflectionResolution: 1.3→70 Å / Num. obs: 40375 / % possible obs: 96.2 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.096 / Χ2: 1.795 / Net I/σ(I): 8.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.3-1.353.10.2830890.89874.1
1.35-1.44.10.27637770.91790.6
1.4-1.465.30.25240740.99997.3
1.46-1.546.20.21141471.06799.5
1.54-1.646.70.17641811.189100
1.64-1.7670.14941951.383100
1.76-1.947.10.12341761.758100
1.94-2.227.20.10142312.113100
2.22-2.87.20.08542082.516100
2.8-706.90.06842973.56199.7

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Phasing

PhasingMethod: sad

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: SAD / Resolution: 1.3→30 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.921 / WRfactor Rfree: 0.22 / WRfactor Rwork: 0.204 / SU B: 1.025 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.069 / ESU R Free: 0.066
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Programs arp/warp, coot, molprobity were also used in refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.226 2052 5.1 %RANDOM
Rwork0.21 ---
all0.211 ---
obs-40353 95.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 7.181 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20.25 Å2
2---0.13 Å20 Å2
3---0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1668 0 27 135 1830
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211747
X-RAY DIFFRACTIONr_bond_other_d0.0030.021154
X-RAY DIFFRACTIONr_angle_refined_deg1.3171.9582383
X-RAY DIFFRACTIONr_angle_other_deg0.89932790
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6565218
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.04722.59777
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.06415255
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2581511
X-RAY DIFFRACTIONr_chiral_restr0.0820.2255
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021973
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02392
X-RAY DIFFRACTIONr_nbd_refined0.2020.2351
X-RAY DIFFRACTIONr_nbd_other0.190.21181
X-RAY DIFFRACTIONr_nbtor_refined0.1840.2849
X-RAY DIFFRACTIONr_nbtor_other0.0850.2838
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0880.298
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.250.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0840.215
X-RAY DIFFRACTIONr_mcbond_it1.60221155
X-RAY DIFFRACTIONr_mcbond_other0.5262439
X-RAY DIFFRACTIONr_mcangle_it1.91431704
X-RAY DIFFRACTIONr_scbond_it1.6882777
X-RAY DIFFRACTIONr_scangle_it2.2713676
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3-1.3340.2721090.2621914306665.982
1.334-1.3710.3391280.2532483303686.001
1.371-1.410.2931220.242612292793.406
1.41-1.4540.2361410.2272630285097.228
1.454-1.5010.241390.2112610277299.17
1.501-1.5540.2181380.2072541268399.851
1.554-1.6120.221330.20324332566100
1.612-1.6780.2331220.20223582480100
1.678-1.7520.2591320.19322682400100
1.752-1.8370.221390.20221552294100
1.837-1.9360.231950.19920582153100
1.936-2.0530.181050.19719552060100
2.053-2.1940.1951020.19518371939100
2.194-2.3690.207800.20317371817100
2.369-2.5940.234940.20315711665100
2.594-2.8970.232770.211449152799.935
2.897-3.340.217610.2112701331100
3.34-4.0780.201590.210831142100
4.078-5.7150.18390.2185689699.888
5.715-300.287370.348152598.667

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