[English] 日本語
Yorodumi
- PDB-3lst: Crystal Structure of CalO1, Methyltransferase in Calicheamicin Bi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3lst
TitleCrystal Structure of CalO1, Methyltransferase in Calicheamicin Biosynthesis, SAH bound form
ComponentsCalO1 Methyltransferase
KeywordsTRANSFERASE / Calicheamicin / Methyltransferase / CalO1 / enediyne / SAH / Structural Genomics / PSI-2 / Protein Structure Initiative / Center for Eukaryotic Structural Genomics / CESG
Function / homology
Function and homology information


O-methyltransferase activity / methylation
Similarity search - Function
O-methyltransferase domain / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / O-methyltransferase COMT-type / Vaccinia Virus protein VP39 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily ...O-methyltransferase domain / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / O-methyltransferase COMT-type / Vaccinia Virus protein VP39 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / CalO1
Similarity search - Component
Biological speciesMicromonospora echinospora (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsChang, A. / Singh, S. / Bingman, C.A. / Thorson, J.S. / Phillips Jr., G.N. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2011
Title: Structural characterization of CalO1: a putative orsellinic acid methyltransferase in the calicheamicin-biosynthetic pathway.
Authors: Chang, A. / Singh, S. / Bingman, C.A. / Thorson, J.S. / Phillips, G.N.
History
DepositionFeb 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CalO1 Methyltransferase
B: CalO1 Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,7656
Polymers75,8722
Non-polymers8934
Water3,261181
1
A: CalO1 Methyltransferase
hetero molecules

A: CalO1 Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,7656
Polymers75,8722
Non-polymers8934
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area8500 Å2
ΔGint-53 kcal/mol
Surface area26120 Å2
MethodPISA
2
B: CalO1 Methyltransferase
hetero molecules

B: CalO1 Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,7656
Polymers75,8722
Non-polymers8934
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area8920 Å2
ΔGint-51 kcal/mol
Surface area25980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.515, 93.603, 240.971
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-398-

HOH

21B-429-

HOH

DetailsThe biological unit is a dimer. There are half of 2 biological units in the asymmetric unit. The dimer generated from the monomer in the asymmetric unit by the operations: x, -y,-z and -x, y,-z+1/2

-
Components

#1: Protein CalO1 Methyltransferase


Mass: 37936.082 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora echinospora (bacteria) / Gene: calO1 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): B834 P(RARE2) / References: UniProt: Q8KNE5
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Protein Solution 20mg/ml CalO1 protein, 20mM Tris pH 8, mixed in a 1:1 ratio with the well solution 20% MEPEG 5K, 0.2M Glycine, 0.1M BTP pH 7.0. Cryoprotected with 20% ethylene glycol, 20% ...Details: Protein Solution 20mg/ml CalO1 protein, 20mM Tris pH 8, mixed in a 1:1 ratio with the well solution 20% MEPEG 5K, 0.2M Glycine, 0.1M BTP pH 7.0. Cryoprotected with 20% ethylene glycol, 20% MEPEG 5K, 0.2M Glycine, 0.1M BTP pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9794, 0.9641
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 6, 2009 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double Crystal Monochromater / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.96411
ReflectionRedundancy: 12.3 % / Av σ(I) over netI: 22.53 / Number: 344828 / Rmerge(I) obs: 0.12 / Χ2: 1.39 / D res high: 2.4 Å / D res low: 50 Å / Num. obs: 28057 / % possible obs: 97.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.515099.810.0723.33713.4
5.176.5110010.0882.03513.8
4.525.1710010.0841.57113.5
4.14.5210010.0881.31413.1
3.814.199.910.0851.27913
3.583.8110010.0931.23613.1
3.413.5810010.1111.19213
3.263.4110010.131.10412.9
3.133.2610010.1561.17213.1
3.023.1310010.1911.18512.8
2.933.0210010.2081.2613
2.852.9310010.2431.15112.9
2.772.8510010.2921.20412.6
2.72.7710010.3331.18312.4
2.642.799.210.3691.09211.5
2.592.6497.610.4041.12811.1
2.532.5995.210.4041.15510.3
2.492.5391.210.4371.13410.1
2.442.4987.710.5131.1079.5
2.42.4483.410.5251.0519
ReflectionResolution: 2.4→50 Å / Num. obs: 28057 / % possible obs: 97.7 % / Redundancy: 12.3 % / Rmerge(I) obs: 0.12 / Χ2: 1.387 / Net I/σ(I): 9.7
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 9 % / Rmerge(I) obs: 0.525 / Num. unique all: 1182 / Χ2: 1.051 / % possible all: 83.4

-
Phasing

PhasingMethod: MAD
Phasing MADD res high: 2.4 Å / D res low: 48.17 Å / FOM acentric: 0.462 / FOM centric: 0.305 / Reflection acentric: 25104 / Reflection centric: 2856
Phasing MAD set
IDR cullis acentricR cullis centricHighest resolution (Å)Lowest resolution (Å)Reflection acentricReflection centric
ISO_1002.448.17251042856
ISO_20.8730.8652.448.17244682820
ANO_10.64802.448.17246800
ANO_20.86502.448.17239120
Phasing MAD set shell
IDResolution (Å)R cullis acentricR cullis centricReflection acentricReflection centric
ISO_110.49-48.1700253142
ISO_17.51-10.4900492149
ISO_16.15-7.5100650142
ISO_15.34-6.1500787136
ISO_14.78-5.3400884152
ISO_14.37-4.7800986148
ISO_14.05-4.37001085141
ISO_13.79-4.05001170154
ISO_13.57-3.79001274141
ISO_13.39-3.57001328151
ISO_13.23-3.39001404144
ISO_13.1-3.23001456156
ISO_12.97-3.1001523137
ISO_12.87-2.97001590153
ISO_12.77-2.87001666144
ISO_12.68-2.77001704146
ISO_12.6-2.68001762147
ISO_12.53-2.6001725142
ISO_12.46-2.53001694109
ISO_12.4-2.46001671122
ANO_110.49-48.170.20802530
ANO_17.51-10.490.19104920
ANO_16.15-7.510.206500
ANO_15.34-6.150.26307870
ANO_14.78-5.340.31108840
ANO_14.37-4.780.40909860
ANO_14.05-4.370.453010840
ANO_13.79-4.050.466011700
ANO_13.57-3.790.546012740
ANO_13.39-3.570.6013280
ANO_13.23-3.390.696014040
ANO_13.1-3.230.733014560
ANO_12.97-3.10.782015230
ANO_12.87-2.970.845015900
ANO_12.77-2.870.879016640
ANO_12.68-2.770.91016880
ANO_12.6-2.680.942017220
ANO_12.53-2.60.959016560
ANO_12.46-2.530.965015770
ANO_12.4-2.460.975014920
ISO_210.49-48.170.590.676253142
ISO_27.51-10.490.6670.849492149
ISO_26.15-7.510.7070.69650142
ISO_25.34-6.150.7570.793787136
ISO_24.78-5.340.7560.773884152
ISO_24.37-4.780.7870.808986148
ISO_24.05-4.370.8070.8331085141
ISO_23.79-4.050.8460.8791169154
ISO_23.57-3.790.8550.8311274141
ISO_23.39-3.570.8530.8761327151
ISO_23.23-3.390.8610.8361404144
ISO_23.1-3.230.8650.91456156
ISO_22.97-3.10.8770.8611520137
ISO_22.87-2.970.8980.9431587153
ISO_22.77-2.870.8970.931665143
ISO_22.68-2.770.9230.941687146
ISO_22.6-2.680.9540.9711706137
ISO_22.53-2.60.9671.0231603135
ISO_22.46-2.530.9881.0261506100
ISO_22.4-2.460.9420.9851427113
ANO_210.49-48.170.24202530
ANO_27.51-10.490.25304920
ANO_26.15-7.510.28306500
ANO_25.34-6.150.37807870
ANO_24.78-5.340.42608840
ANO_24.37-4.780.56109860
ANO_24.05-4.370.605010850
ANO_23.79-4.050.675011690
ANO_23.57-3.790.775012740
ANO_23.39-3.570.809013270
ANO_23.23-3.390.893014040
ANO_23.1-3.230.918014560
ANO_22.97-3.10.939015200
ANO_22.87-2.970.959015870
ANO_22.77-2.870.976016550
ANO_22.68-2.770.981016800
ANO_22.6-2.680.986016300
ANO_22.53-2.60.99014630
ANO_22.46-2.530.994013570
ANO_22.4-2.460.995012530
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
111.584-10.507-109.343SE31.730.8
220.946-14.61-121.932SE45.760.86
36.052-6.327-113.361SE60.460.96
429.513-31.974-234.832SE49.10.93
513.234-15.18-106.682SE57.080.87
69.9-8.256-113.346SE45.070.95
712.072-0.981-25.832SE39.40.87
829.118-39.933-129.084SE70.020.88
927.999-12.541-51.622SE82.190.98
1028.837-8.642-49.804SE43.560.84
1114.908-23.274-87.555SE69.290.91
1225.496-5.275-40.249SE71.80.81
1326.902-20.95-50.362SE58.680.8
1421.364-12.286-45.572SE60.320.86
1530.704-16.175-76.251SE44.40.71
1626.112-37.974-225.473SE791.01
1724.143-2.438-167.756SE43.810.63
1830.69-29.678-230.421SE67.330.72
1923.911-23.059-54.566SE62.30.71
204.751-1.959-9.237SE76.430.87
2129.967-17.543-40.136SE98.660.64
2226.151-6.473-46.189SE40.510.42
2326.8279.71646.509SE64.360.45
241.0049.473169.403SE10.05
Phasing MAD shell
Resolution (Å)FOM acentricFOM centricReflection acentricReflection centric
10.49-48.170.8890.652253142
7.51-10.490.8720.632492149
6.15-7.510.8530.568650142
5.34-6.150.8040.508787136
4.78-5.340.760.456884152
4.37-4.780.6930.411986148
4.05-4.370.6680.361085141
3.79-4.050.6580.3111170154
3.57-3.790.6050.3111274141
3.39-3.570.5710.2821328151
3.23-3.390.5120.2591404144
3.1-3.230.4930.2091456156
2.97-3.10.4460.1821523137
2.87-2.970.4050.161590153
2.77-2.870.3530.1421666144
2.68-2.770.3130.1351704146
2.6-2.680.2580.1371762147
2.53-2.60.2320.1061725142
2.46-2.530.2080.0981694109
2.4-2.460.1770.1161671122

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
PHENIX1.5_2refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.4→48.174 Å / Occupancy max: 1 / Occupancy min: 0.46 / SU ML: 0.38 / σ(F): 1.32 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.251 1411 5.05 %
Rwork0.2 --
obs0.203 27959 97.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40 Å2 / ksol: 0.334 e/Å3
Displacement parametersBiso max: 210.78 Å2 / Biso mean: 51.029 Å2 / Biso min: 13.71 Å2
Baniso -1Baniso -2Baniso -3
1-0.508 Å2-0 Å20 Å2
2---2.326 Å2-0 Å2
3---1.891 Å2
Refinement stepCycle: LAST / Resolution: 2.4→48.174 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5020 0 60 181 5261
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045222
X-RAY DIFFRACTIONf_angle_d0.7177098
X-RAY DIFFRACTIONf_chiral_restr0.049808
X-RAY DIFFRACTIONf_plane_restr0.002938
X-RAY DIFFRACTIONf_dihedral_angle_d14.8931882
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.4860.3031220.2592280240286
2.486-2.5850.331440.2452503264793
2.585-2.7030.3311260.252639276599
2.703-2.8450.281590.22926712830100
2.845-3.0240.2851300.22227082838100
3.024-3.2570.291520.22826652817100
3.257-3.5850.2371310.21727432874100
3.585-4.1030.2351380.16927212859100
4.103-5.1690.2051420.14527712913100
5.169-48.1830.2041670.17328473014100

+
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