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- PDB-4rfq: Human Methyltransferase-Like 18 -

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Basic information

Entry
Database: PDB / ID: 4rfq
TitleHuman Methyltransferase-Like 18
ComponentsHistidine protein methyltransferase 1 homolog
KeywordsTRANSFERASE / structural genomics / Structural Genomics Consortium / SGC
Function / homologypeptidyl-histidine methylation, to form tele-methylhistidine / protein-L-histidine N-tele-methyltransferase activity / Methyltransferase domain / heat shock protein binding / Transferases; Transferring one-carbon groups; Methyltransferases / S-adenosyl-L-methionine-dependent methyltransferase superfamily / protein-containing complex / S-ADENOSYLMETHIONINE / Histidine protein methyltransferase 1 homolog
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsTempel, W. / Ravichandran, M. / Li, Y. / Walker, J.R. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Brown, P.J. / Hong, B.S. / Structural Genomics Consortium (SGC)
CitationJournal: TO BE PUBLISHED
Title: Human Methyltransferase-Like 18
Authors: Ravichandran, M. / Tempel, W. / Li, Y. / Walker, J.R. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Brown, P.J. / Hong, B.S.
History
DepositionSep 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histidine protein methyltransferase 1 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,47014
Polymers33,0711
Non-polymers39813
Water39622
1
A: Histidine protein methyltransferase 1 homolog
hetero molecules

A: Histidine protein methyltransferase 1 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,93928
Polymers66,1422
Non-polymers79726
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area3440 Å2
ΔGint-21 kcal/mol
Surface area22290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.150, 70.150, 170.688
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
DetailsAUTHORS STATE THAT THE BIOLOGICAL ASSEMBLY HAS NOT BEEN DETERMINED AS PART OF THIS STUDY.

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Components

#1: Protein Histidine protein methyltransferase 1 homolog / Arsenic-transactivated protein 2 / AsTP2 / Methyltransferase-like protein 18


Mass: 33071.176 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 63-372 / Mutation: delta(143-161)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: METTL18, ASTP2, C1orf156 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) V2R-pRARE
References: UniProt: O95568, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 12 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 3.17 Å3/Da / Density % sol: 61.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.6
Details: 2.0 M ammonium sulfate, 0.2 M potassium/sodium tartrate, 0.1 M sodium citrate, 0.005 M taurine, 0.005 M SAM, pH 5.6, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 17502 / % possible obs: 100 % / Redundancy: 13.5 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 14.4
Reflection shell

Rmerge(I) obs: 0.01 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique all% possible all
2.4-2.4914.52.5261301803100
8.98-47.6310.231.6417641199

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
Aimless0.3.8data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.14data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: from isomorphous crystal

Resolution: 2.4→47.63 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.2393 / WRfactor Rwork: 0.1939 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8296 / SU B: 15.328 / SU ML: 0.171 / SU R Cruickshank DPI: 0.2459 / SU Rfree: 0.2077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.246 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THE STRUCTURE OF AN ISOMORPHOUS CRYSTAL WAS SOLVED BY MOLECULAR REPLACEMENT WITH PHASER AND A COORDINATE ENSEMBLE BASED ON PDB ENTRIES 4QPN AND 4MTL. DENSITY MODIFICATION WITH PARROT, ...Details: THE STRUCTURE OF AN ISOMORPHOUS CRYSTAL WAS SOLVED BY MOLECULAR REPLACEMENT WITH PHASER AND A COORDINATE ENSEMBLE BASED ON PDB ENTRIES 4QPN AND 4MTL. DENSITY MODIFICATION WITH PARROT, AUTOMATED MODEL BUILDING WITH BUCCUANEER, DENSITY MODIFICATION WITH DM PRODUCED A MAP FOR REAL SPACE REFINEMENT AND PRUNING OF A FFAS03/SCWRL MODEL BASED ON PDB ENTRY 4QPN. ARP/WARP DUMMY ATOM-BASED DENSITY MODIFICATION, SEVERAL ITERATIONS OF PARROT DENSITY MODIFICATION/BUCCANEER AUTO-BUILDING AND AUTO-BUILDING IN ARP/WARP FOLLOWED. COOT WAS USED FOR INTERACTIVE MODEL BUILDING. MODEL GEOMETRY WAS EVALUATED WITH MOLPROBITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2378 875 5 %RANDOM
Rwork0.1966 ---
obs0.1987 17434 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 148.23 Å2 / Biso mean: 63.541 Å2 / Biso min: 38.29 Å2
Baniso -1Baniso -2Baniso -3
1--1.7 Å20 Å20 Å2
2---1.7 Å20 Å2
3---3.41 Å2
Refinement stepCycle: LAST / Resolution: 2.4→47.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2055 0 39 22 2116
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192132
X-RAY DIFFRACTIONr_bond_other_d0.0010.022032
X-RAY DIFFRACTIONr_angle_refined_deg1.3681.9842889
X-RAY DIFFRACTIONr_angle_other_deg0.71334674
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3565269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.56724.23178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.49615356
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.773156
X-RAY DIFFRACTIONr_chiral_restr0.0730.2335
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212365
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02473
X-RAY DIFFRACTIONr_mcbond_it2.5143.1771079
X-RAY DIFFRACTIONr_mcbond_other2.5143.1771079
X-RAY DIFFRACTIONr_mcangle_it3.8454.7581345
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 70 -
Rwork0.292 1189 -
all-1259 -
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)
110.01926.9559-0.68125.16280.6277.917-0.14620.50320.4805-0.32750.38440.5389-0.1761-1.1232-0.23820.5998-0.0069-0.04320.46490.27080.5339-3.9765.17525.28
24.25130.2202-1.15742.3979-0.26032.41390.0865-0.52350.13910.20380.10180.0232-0.1466-0.0243-0.18830.3513-0.0230.18430.1019-0.01390.24279.4718.12540.17
33.50220.2283-0.08343.7588-0.13612.68830.10810.08510.0396-0.3515-0.0182-0.22860.02890.0931-0.08990.3750.03190.24130.0090.02580.225116.6285.15124.385
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A69 - 95
2X-RAY DIFFRACTION2A96 - 239
3X-RAY DIFFRACTION3A253 - 370

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