[English] 日本語
Yorodumi
- PDB-3otg: Crystal Structure of CalG1, Calicheamicin Glycostyltransferase, T... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3otg
TitleCrystal Structure of CalG1, Calicheamicin Glycostyltransferase, TDP bound form
ComponentsCalG1
KeywordsTRANSFERASE / Calicheamicin / TDP / Structural Genomics / PSI-2 / Protein Structure Initiative / Center for Eukaryotic Structural Genomics / CESG / GT-B fold / Glycosyltransferase / Enzyme Discovery for Natural Product Biosynthesis / NatPro
Function / homology
Function and homology information


UDP-glycosyltransferase activity / hexosyltransferase activity / antibiotic biosynthetic process
Similarity search - Function
Glycosyltransferase family 28 N-terminal domain / : / Erythromycin biosynthesis protein CIII-like, N-terminal domain / Erythromycin biosynthesis protein CIII-like, central / : / Erythromycin biosynthesis protein CIII-like, C-terminal domain / UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase / Glycogen Phosphorylase B; / Rossmann fold ...Glycosyltransferase family 28 N-terminal domain / : / Erythromycin biosynthesis protein CIII-like, N-terminal domain / Erythromycin biosynthesis protein CIII-like, central / : / Erythromycin biosynthesis protein CIII-like, C-terminal domain / UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
THYMIDINE-5'-DIPHOSPHATE / CalG1
Similarity search - Component
Biological speciesMicromonospora echinospora (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.08 Å
AuthorsChang, A. / Singh, S. / Bingman, C.A. / Thorson, J.S. / Phillips Jr., G.N. / Center for Eukaryotic Structural Genomics (CESG) / Enzyme Discovery for Natural Product Biosynthesis (NatPro)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Complete set of glycosyltransferase structures in the calicheamicin biosynthetic pathway reveals the origin of regiospecificity.
Authors: Chang, A. / Singh, S. / Helmich, K.E. / Goff, R.D. / Bingman, C.A. / Thorson, J.S. / Phillips, G.N.
History
DepositionSep 11, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 2, 2011Group: Database references
Revision 1.3Aug 8, 2012Group: Structure summary
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software
Revision 1.5Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CalG1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3147
Polymers43,7351
Non-polymers5796
Water5,639313
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: CalG1
hetero molecules

A: CalG1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,62814
Polymers87,4692
Non-polymers1,15912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Buried area4520 Å2
ΔGint-109 kcal/mol
Surface area32570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.177, 106.177, 155.817
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

-
Components

#1: Protein CalG1


Mass: 43734.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora echinospora (bacteria) / Gene: calG1, Q8KNF2 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): B834 P(RARE2) / References: UniProt: Q8KNF2
#2: Chemical ChemComp-TYD / THYMIDINE-5'-DIPHOSPHATE


Mass: 402.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O11P2
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: Protein Solution (20mg/ml CalG1 protein, 20mM Tris pH 8) mixed in a 1:1 ratio with the well solution (20% PEG3350, 0.2M LiSO4, 100mM BisTris pH 6.5) Cryoprotected with 20% ethylene glycol, ...Details: Protein Solution (20mg/ml CalG1 protein, 20mM Tris pH 8) mixed in a 1:1 ratio with the well solution (20% PEG3350, 0.2M LiSO4, 100mM BisTris pH 6.5) Cryoprotected with 20% ethylene glycol, 20% PEG3350, 0.2M LiSO4, 100mM BisTris pH 6.5, vapor diffusion, hanging drop, temperature 298K, VAPOR DIFFUSION, HANGING DROP

-
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: Oct 18, 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: 41.9 % / Av σ(I) over netI: 62.35 / Number: 1281384 / Rmerge(I) obs: 0.082 / Χ2: 1.31 / D res high: 2.11 Å / D res low: 50 Å / Num. obs: 30569 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.725099.610.0422.16538
4.545.7299.910.0471.87441.4
3.974.5410010.0611.22342
3.613.9710010.0611.08342.4
3.353.6110010.0551.15442.7
3.153.3510010.0681.19342.8
2.993.1510010.0911.14143.1
2.862.9910010.1171.15943
2.752.8610010.1391.16143.2
2.662.7510010.1661.16843.3
2.582.6610010.1891.19343.2
2.52.5810010.2271.19143.3
2.442.510010.2791.22143.4
2.382.4410010.3511.25143.2
2.322.3810010.4111.29843.4
2.272.3210010.4681.33743.1
2.232.2710010.5811.44142.6
2.192.2310010.6531.26941.9
2.152.1910010.7661.34140.1
2.112.1599.710.8141.23932.7
ReflectionResolution: 2.08→50 Å / Num. obs: 31794 / % possible obs: 100 % / Redundancy: 41.9 % / Rmerge(I) obs: 0.082 / Χ2: 1.306 / Net I/σ(I): 12.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.11-2.1532.70.81414741.239199.7
2.15-2.1940.10.76614941.3411100
2.19-2.2341.90.65314911.2691100
2.23-2.2742.60.58115141.4411100
2.27-2.3243.10.46814911.3371100
2.32-2.3843.40.41114861.2981100
2.38-2.4443.20.35115181.2511100
2.44-2.543.40.27914921.2211100
2.5-2.5843.30.22715081.1911100
2.58-2.6643.20.18915231.1931100
2.66-2.7543.30.16614911.1681100
2.75-2.8643.20.13915261.1611100
2.86-2.99430.11715241.1591100
2.99-3.1543.10.09115221.1411100
3.15-3.3542.80.06815281.1931100
3.35-3.6142.70.05515421.1541100
3.61-3.9742.40.06115471.0831100
3.97-4.54420.06115721.2231100
4.54-5.7241.40.04716011.874199.9
5.72-50380.04217252.165199.6

-
Phasing

PhasingMethod: MAD
Phasing MADD res high: 2.08 Å / D res low: 45.98 Å / FOM acentric: 0.505 / FOM centric: 0.29 / Reflection acentric: 27188 / Reflection centric: 4610
Phasing MAD set
IDR cullis acentricR cullis centricHighest resolution (Å)Lowest resolution (Å)Reflection acentricReflection centric
ISO_1002.0845.98259554477
ISO_20.8280.8052.0845.98258684468
ANO_10.58502.0845.98259520
ANO_20.80202.0845.98270890
Phasing MAD set shell
IDResolution (Å)R cullis acentricR cullis centricReflection acentricReflection centric
ISO_19.13-45.9800239218
ISO_16.52-9.1300496229
ISO_15.34-6.5200674226
ISO_14.63-5.3400812233
ISO_14.15-4.6300941233
ISO_13.79-4.15001036227
ISO_13.51-3.79001150233
ISO_13.28-3.51001240228
ISO_13.1-3.28001323233
ISO_12.94-3.1001406228
ISO_12.8-2.94001483229
ISO_12.68-2.8001561238
ISO_12.58-2.68001625236
ISO_12.49-2.58001696222
ISO_12.4-2.49001762239
ISO_12.32-2.4001816223
ISO_12.26-2.32001877238
ISO_12.19-2.26001924231
ISO_12.13-2.19002017232
ISO_12.08-2.1300877101
ANO_19.13-45.980.1502390
ANO_16.52-9.130.13204960
ANO_15.34-6.520.12706740
ANO_14.63-5.340.17908120
ANO_14.15-4.630.27209410
ANO_13.79-4.150.32010360
ANO_13.51-3.790.318011500
ANO_13.28-3.510.339012400
ANO_13.1-3.280.385013230
ANO_12.94-3.10.489014060
ANO_12.8-2.940.552014830
ANO_12.68-2.80.645015610
ANO_12.58-2.680.723016250
ANO_12.49-2.580.767016960
ANO_12.4-2.490.83017620
ANO_12.32-2.40.875018160
ANO_12.26-2.320.905018770
ANO_12.19-2.260.935019240
ANO_12.13-2.190.962020170
ANO_12.08-2.130.96808740
ISO_29.13-45.980.6560.652239217
ISO_26.52-9.130.6860.68496229
ISO_25.34-6.520.7330.684674226
ISO_24.63-5.340.7860.806812233
ISO_24.15-4.630.8290.865941233
ISO_23.79-4.150.8280.8591036227
ISO_23.51-3.790.8780.8561150233
ISO_23.28-3.510.8650.8431240228
ISO_23.1-3.280.8630.8741323233
ISO_22.94-3.10.8660.8321404227
ISO_22.8-2.940.8730.8521478228
ISO_22.68-2.80.8610.8731553238
ISO_22.58-2.680.8680.8611621236
ISO_22.49-2.580.8670.8721690222
ISO_22.4-2.490.8490.861754238
ISO_22.32-2.40.8440.8761809223
ISO_22.26-2.320.8420.8691864236
ISO_22.19-2.260.8170.821909230
ISO_22.13-2.190.8290.8912003230
ISO_22.08-2.130.9311.031872101
ANO_29.13-45.980.19202390
ANO_26.52-9.130.15304960
ANO_25.34-6.520.16106740
ANO_24.63-5.340.22608120
ANO_24.15-4.630.31309410
ANO_23.79-4.150.387010360
ANO_23.51-3.790.422011500
ANO_23.28-3.510.482012410
ANO_23.1-3.280.569013240
ANO_22.94-3.10.706014040
ANO_22.8-2.940.757014810
ANO_22.68-2.80.833015550
ANO_22.58-2.680.872016250
ANO_22.49-2.580.897016930
ANO_22.4-2.490.946017610
ANO_22.32-2.40.952018150
ANO_22.26-2.320.965018750
ANO_22.19-2.260.975019260
ANO_22.13-2.190.988020100
ANO_22.08-2.130.991020310
Phasing MAD shell
Resolution (Å)FOM acentricFOM centricReflection acentricReflection centric
9.13-45.980.8840.595239218
6.52-9.130.8440.566496229
5.34-6.520.850.547674226
4.63-5.340.7910.453812234
4.15-4.630.7330.375941234
3.79-4.150.70.351036227
3.51-3.790.6960.3061150234
3.28-3.510.6870.3371241229
3.1-3.280.6920.2771324233
2.94-3.10.6310.2991406229
2.8-2.940.6190.2741486229
2.68-2.80.5740.2341563238
2.58-2.680.5250.2281629236
2.49-2.580.4940.1921699223
2.4-2.490.440.1661769240
2.32-2.40.3910.1371822223
2.26-2.320.3370.1591888239
2.19-2.260.2880.1221941231
2.13-2.190.2440.1162024232
2.08-2.130.1590.0952048226

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.08→45.976 Å / Occupancy max: 1 / Occupancy min: 0.41 / SU ML: 0.28 / σ(F): 1.33 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.227 1607 5.05 %
Rwork0.1926 --
obs0.1943 31794 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.984 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso max: 224.14 Å2 / Biso mean: 49.9016 Å2 / Biso min: 19.66 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.08→45.976 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2906 0 30 313 3249
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063086
X-RAY DIFFRACTIONf_angle_d1.0054220
X-RAY DIFFRACTIONf_chiral_restr0.062469
X-RAY DIFFRACTIONf_plane_restr0.005570
X-RAY DIFFRACTIONf_dihedral_angle_d13.9251131
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.08-2.14720.25361540.22322646280099
2.1472-2.22390.21921320.221727022834100
2.2239-2.3130.25281410.221326972838100
2.313-2.41820.24151370.212327202857100
2.4182-2.54570.24951430.207726882831100
2.5457-2.70520.26711420.207927202862100
2.7052-2.9140.26141530.21527162869100
2.914-3.20720.261440.208127462890100
3.2072-3.67110.22331470.187227652912100
3.6711-4.62450.15341540.150428122966100
4.6245-45.98720.22191600.17129753135100

+
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