[English] 日本語
Yorodumi
- PDB-6xi5: Crystal structure of human N-acetylserotonin O-methyltransferase-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6xi5
TitleCrystal structure of human N-acetylserotonin O-methyltransferase-like protein soaked with PDHPTAO
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: 2.61 Å
AuthorsStogios, P.J. / Evdokimova, E. / Yakunin, A. / Savchenko, A.
CitationJournal: To Be Published
Title: Crystal structure of human N-acetylserotonin O-methyltransferase-like protein soaked with PDHPTAO
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)51,8314
Polymers51,6392
Non-polymers1922
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-38 kcal/mol
Surface area19150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.733, 82.860, 117.232
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

-
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-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.44 %
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 PDHPTAO was added to the crystallization drop and let to soak for 2.5 hours

-
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 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 15701 / % possible obs: 98.3 % / Redundancy: 5 % / Biso Wilson estimate: 71.62 Å2 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.042 / Net I/σ(I): 28.03
Reflection shellResolution: 2.6→2.64 Å / Rmerge(I) obs: 1.188 / Mean I/σ(I) obs: 1.87 / Num. unique obs: 757 / CC1/2: 0.571 / Rpim(I) all: 0.568 / % possible all: 99.3

-
Processing

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

2p5x


Resolution: 2.61→29.31 Å / SU ML: 0.3254 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.4056
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2928 784 5.01 %RANDOM
Rwork0.2407 14872 --
obs0.2433 15656 98.04 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 100.82 Å2
Refinement stepCycle: LAST / Resolution: 2.61→29.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3220 0 10 24 3254
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00413294
X-RAY DIFFRACTIONf_angle_d0.78944444
X-RAY DIFFRACTIONf_chiral_restr0.0484492
X-RAY DIFFRACTIONf_plane_restr0.0039566
X-RAY DIFFRACTIONf_dihedral_angle_d22.97721222
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.61-2.770.37211270.3532415X-RAY DIFFRACTION97.96
2.77-2.980.3571300.31872463X-RAY DIFFRACTION99.5
2.98-3.280.32851310.27422489X-RAY DIFFRACTION99.47
3.28-3.760.31251320.24612501X-RAY DIFFRACTION99.21
3.76-4.730.26451320.20982501X-RAY DIFFRACTION98.47
4.73-29.310.27631320.22672503X-RAY DIFFRACTION93.97
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)
15.32320102077-4.49906826878-5.194774661934.143651385124.437048171725.11564430836-0.738422406211-0.434949917634-1.571437166751.74865010583-0.1659296099350.9064078948471.4365946684-0.2223581122730.8698337616231.038757020840.0410168011863-0.03080355899040.7628548256050.07849689565830.8791372402070.43772484736780.612630351731.2727081919
24.862965703423.97567250659-0.3055109146284.4237407064-3.337317155138.224900372710.5280508881380.5898936741491.092549037060.909061789282-0.584084945849-3.84244315446-0.6597512314341.830254004470.02509594280590.732564783033-0.14012966201-0.1645627608980.882677532096-0.09065107952011.0491500332713.840345281795.361578559219.8213481448
31.606503093320.2297166542260.7330299707956.599407754555.636346039137.750384953740.1598447524720.0986556574815-0.378405236561-0.7380854648570.285483488825-0.653473539138-0.5290009994320.680245562246-0.3683427664740.597375424051-0.1088067884340.07483544592830.652449638564-0.07735928936960.5643571700355.8557454352686.312560031621.0606000901
40.2556859647260.2820404470630.9052407457355.199523297722.145850655524.535128853410.907917023373-0.03181470540471.04646683699-0.348529635756-0.164205857226-2.95971952557-0.259682845742.32105837211-0.6042807147890.671644073452-0.357483745428-0.04352130798581.73140276015-0.3993774692571.2342809840618.5969463262101.84396849336.2883399135
52.9635245647-1.98762105757-0.9109216695316.155543703593.376122739764.941681735510.09885998318850.0471376374031-0.106216652339-0.784589675496-0.6441537846250.635639196644-0.690304782542-0.6447670108330.6837613342880.805428460059-0.0641612355336-0.02121845975530.568730182087-0.00682488530870.5465257672470.90669065062592.092734399523.1488143174
63.80192278232-0.8253766318823.943528544149.115047417860.6700055274074.32065192536-0.329541850475-0.608508213074-1.350377471950.5766597806661.02676443798-1.880497181130.05674581904691.15838922443-0.722932576440.9965488303870.139302268765-0.1674305953331.3768790515-0.001784933737061.279051524115.724845853598.017485964745.8985599304
75.384172475050.6803377618260.323709680543.84848549453.111449818217.493476880010.113066732130.7750447526180.1111561797030.617371555736-0.0955520225851.123578024180.978748734777-0.0271015666576-0.09521399484940.6607196547080.0461637813284-0.05674734243050.685077566539-0.0003597573160790.56495185254-4.9615626749794.134485248832.825342936
87.01677652474-2.255678275130.9733711178866.02559456730.7040055156187.213685391410.51550045321-0.368716714479-0.8284044804420.860576109987-0.242317358342-0.1356891076560.924473564818-0.151206907231-0.2687392595320.82992721099-0.109502158549-0.1390617685410.5337883562560.07373312511590.559875927562-0.98889513864897.59082476867.62651073
98.977114265641.723213043970.5694389557035.060297360011.544271773583.978391457980.304640325469-0.94691577629-0.4456871663650.20285244835-0.2909183579560.5139364087730.966078021207-1.34845597765-0.07242369247490.658708386125-0.02909016638040.004754720899490.602777113472-0.01843629518910.70186463912-12.214413914696.824167881258.050797685
103.88674793497-1.049395930961.569745972454.6024660677-1.242690180665.78584178037-0.03532625444240.0490942923203-0.493706652224-0.06247012751010.009434573795620.0113998911249-0.1424720020390.120826805491-0.04125571713940.712942735340.04303799700380.03327855272040.5663593254970.02304884597370.580466600772-3.533857852798.858508992455.3057092836
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 40 )
2X-RAY DIFFRACTION2chain 'A' and (resid 41 through 53 )
3X-RAY DIFFRACTION3chain 'A' and (resid 54 through 93 )
4X-RAY DIFFRACTION4chain 'A' and (resid 94 through 117 )
5X-RAY DIFFRACTION5chain 'A' and (resid 118 through 152 )
6X-RAY DIFFRACTION6chain 'A' and (resid 153 through 185 )
7X-RAY DIFFRACTION7chain 'A' and (resid 186 through 213 )
8X-RAY DIFFRACTION8chain 'B' and (resid 10 through 77 )
9X-RAY DIFFRACTION9chain 'B' and (resid 78 through 117 )
10X-RAY DIFFRACTION10chain 'B' and (resid 118 through 213 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more