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- PDB-6xi4: Crystal structure of Maf domain of human N-acetylserotonin O-meth... -

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Basic information

Entry
Database: PDB / ID: 6xi4
TitleCrystal structure of Maf domain of human N-acetylserotonin O-methyltransferase-like protein soaked with TFBQ
ComponentsProbable bifunctional dTTP/UTP pyrophosphatase/methyltransferase protein
KeywordsCELL CYCLE / ASMTL
Function / homology
Function and homology information


dTTP diphosphatase activity / UTP diphosphatase activity / nucleotide diphosphatase / nucleoside triphosphate diphosphatase activity / nucleotide metabolic process / O-methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / methylation / cytosol
Similarity search - Function
Nucleoside triphosphate pyrophosphatase Maf-like protein / Maf-like protein / Acetylserotonin O-methyltransferase, dimerisation domain / Dimerisation domain / Inosine triphosphate pyrophosphatase-like / O-methyltransferase domain / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / O-methyltransferase COMT-type / Winged helix DNA-binding domain superfamily ...Nucleoside triphosphate pyrophosphatase Maf-like protein / Maf-like protein / Acetylserotonin O-methyltransferase, dimerisation domain / Dimerisation domain / Inosine triphosphate pyrophosphatase-like / O-methyltransferase domain / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / O-methyltransferase COMT-type / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Probable bifunctional dTTP/UTP pyrophosphatase/methyltransferase protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsStogios, P.J. / Evdokimova, E. / Yakunin, A. / Savchenko, A.
CitationJournal: To Be Published
Title: Crystal structure of Maf domain of human N-acetylserotonin O-methyltransferase-like protein soaked with TFBQ
Authors: Yakunin, A.
History
DepositionJun 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable bifunctional dTTP/UTP pyrophosphatase/methyltransferase protein
B: Probable bifunctional dTTP/UTP pyrophosphatase/methyltransferase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0089
Polymers51,6392
Non-polymers3697
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-89 kcal/mol
Surface area18850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.616, 84.507, 116.673
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

#1: Protein Probable bifunctional dTTP/UTP pyrophosphatase/methyltransferase protein


Mass: 25819.490 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ASMTL / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O95671, nucleotide diphosphatase, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.51 Å3/Da / Density % sol: 51.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Hepes pH 7, 10% (w/v) PEG 5K MME, 5% tacsimate, 2.5 mM MgCl2 and 0.2 mM CoCl2. 10 mM of TFBQ was added to the crystallization drop and let to soak for 2.5 hours

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.22→50 Å / Num. obs: 26360 / % possible obs: 99.4 % / Redundancy: 6.8 % / Biso Wilson estimate: 48.31 Å2 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.035 / Net I/σ(I): 33.22
Reflection shellResolution: 2.22→2.26 Å / Rmerge(I) obs: 1.167 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1235 / CC1/2: 0.522 / Rpim(I) all: 0.548

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Processing

Software
NameVersionClassification
PHENIX1.15_3448refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2P5X

2p5x


Resolution: 2.22→28.69 Å / SU ML: 0.3357 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.854
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2561 1316 5.01 %RANDOM
Rwork0.2325 24977 --
obs0.2337 26293 99.32 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 75.86 Å2
Refinement stepCycle: LAST / Resolution: 2.22→28.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3220 0 15 80 3315
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00343294
X-RAY DIFFRACTIONf_angle_d0.67984444
X-RAY DIFFRACTIONf_chiral_restr0.0429492
X-RAY DIFFRACTIONf_plane_restr0.003566
X-RAY DIFFRACTIONf_dihedral_angle_d20.67821222
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.22-2.310.49331380.42772628X-RAY DIFFRACTION96.58
2.31-2.410.40141450.37052741X-RAY DIFFRACTION99.07
2.41-2.540.33111440.3362725X-RAY DIFFRACTION99.65
2.54-2.70.29611450.30772747X-RAY DIFFRACTION99.59
2.7-2.910.33771460.28952780X-RAY DIFFRACTION99.86
2.91-3.20.26711460.25572780X-RAY DIFFRACTION99.93
3.2-3.660.23241480.22992796X-RAY DIFFRACTION99.83
3.66-4.610.23561480.1932819X-RAY DIFFRACTION99.93
4.61-28.690.20551560.18442961X-RAY DIFFRACTION99.49
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)
12.379043163220.338647085105-0.3152697466917.635663668921.23502265195.406832957440.0245947783862-0.126274993045-0.2786147641580.431812477153-0.114891910408-0.2686621894840.1064221573510.08902207445290.1175199201930.452644879690.002648327880280.01243484508720.375763452204-0.0006217611858920.3840415098765.1268944456987.343811243224.8335640169
29.313341964013.085937114122.511881571454.674051801653.693790409393.018516675570.6368016821570.0107330114536-0.0558762278337-0.1127159175230.514172671589-1.3468123085-0.5219589094972.23404512495-1.016075547720.735107876118-0.145641505883-0.02055087688351.06707667581-0.1872814748410.84409364584218.4222887471103.59794980236.2538062045
32.6391691292-0.320892995562-0.506676878517.537321525712.365116619574.46960803241-0.07889849353040.195767738429-0.0752781046606-0.594841014008-0.140493791230.456391127537-0.349892164233-0.2353059120710.1487507265140.600657704744-0.01130081666070.05289228808590.4528103180150.04453648515230.347141504750.97218848228893.675857978223.19720536
48.07398317625-2.566463309451.934701846518.09822492710.3132504850682.240822292470.0590688846167-1.17100219768-0.7925183876070.5905545947810.459875760009-0.137775352657-0.3049970434531.16871269083-0.5843621253610.7637574898120.0252848076846-0.0473270234111.16597636723-0.02893407891420.89246013705516.152834081499.866047143145.3859003466
58.778918098922.207515410332.602101716737.471472083963.656558677312.37785582630.1027012341020.03607977909-0.6290881663960.3571245230930.09446440499260.193344508887-0.195641011887-0.299131088114-0.1597686538680.7287281104390.01307057720990.08699907225360.4937488925410.02519812647710.409250537886-3.2711470727396.556383278334.2380098584
65.25496425026-1.895403735580.6470238608765.63889678463-0.5935279662797.357081393480.362322278932-0.0461206110127-0.430382672074-0.126373308037-0.177855649408-0.07278188903980.534616505819-0.0104192859269-0.1586086066740.69076982318-0.0166997211028-0.04765588820760.3437700219320.01363197856960.402121725369-1.4630926977199.77507042867.277569274
73.757493472520.301108599972.48642033192.795632554221.504817057149.025447425250.03986903390910.0480921447332-0.383061701450.1077215704310.05618679903320.0628845235316-0.0207273566789-0.0947519182697-0.09862568051720.6294032856560.08847860070180.0494993432630.3486059813010.06094417529220.440559052718-6.4834178352100.42060221355.8037508149
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 93 )
2X-RAY DIFFRACTION2chain 'A' and (resid 94 through 117 )
3X-RAY DIFFRACTION3chain 'A' and (resid 118 through 152 )
4X-RAY DIFFRACTION4chain 'A' and (resid 153 through 181 )
5X-RAY DIFFRACTION5chain 'A' and (resid 182 through 213 )
6X-RAY DIFFRACTION6chain 'B' and (resid 10 through 77 )
7X-RAY DIFFRACTION7chain 'B' and (resid 78 through 213 )

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