[English] 日本語
Yorodumi
- PDB-3ia7: Crystal Structure of CalG4, the Calicheamicin Glycosyltransferase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ia7
TitleCrystal Structure of CalG4, the Calicheamicin Glycosyltransferase
ComponentsCalG4
KeywordsTRANSFERASE / Glycosysltransferase / Calicheamicin / CalG4 / enediyne
Function / homology
Function and homology information


UDP-glycosyltransferase activity / hexosyltransferase activity / biosynthetic process / metal ion binding
Similarity search - Function
UDP-glycosyltransferase, MGT-like / 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
Biological speciesMicromonospora echinospora (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.91 Å
AuthorsChang, A. / Singh, S. / Bingman, C.A. / Thorson, J.S. / Phillips Jr., G.N.
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
DepositionJul 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 2, 2011Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CalG4
B: CalG4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,9655
Polymers88,8502
Non-polymers1163
Water7,873437
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-50 kcal/mol
Surface area32860 Å2
MethodPISA
2
A: CalG4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5003
Polymers44,4251
Non-polymers762
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: CalG4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4652
Polymers44,4251
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.749, 66.966, 86.616
Angle α, β, γ (deg.)90.000, 93.530, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein CalG4


Mass: 44424.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora echinospora (bacteria) / Strain: Micromonospora echinospora / Gene: calG4, Q8KNC3 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): B834 P(RARE2) / References: UniProt: Q8KNC3
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 437 / 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: 2.76 Å3/Da / Density % sol: 55.45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: Protein Solution (10 mg/ml CalG4 Protein, 0.05 M NaCl, 0.005 M Tris pH 8) mixed in a 1:1 ratio with the Well Solution (19% PEG4K, 0.08 M CaCl2, 0.1 M CHES pH 9.5) Cryoprotected with 25% ...Details: Protein Solution (10 mg/ml CalG4 Protein, 0.05 M NaCl, 0.005 M Tris pH 8) mixed in a 1:1 ratio with the Well Solution (19% PEG4K, 0.08 M CaCl2, 0.1 M CHES pH 9.5) Cryoprotected with 25% ethylene glycol, 19% PEG4K, 0.08 M CaCl2, 0.1 M CHES pH 9.5, vapor diffusion, hanging drop, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97945, 0.96421
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 31, 2008 / 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
10.979451
20.964211
ReflectionRedundancy: 7.2 % / Av σ(I) over netI: 21.83 / Number: 537130 / Rmerge(I) obs: 0.074 / Χ2: 1.04 / D res high: 1.91 Å / D res low: 50 Å / Num. obs: 74332 / % possible obs: 98.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.115099.910.0490.9127.6
3.274.1110010.061.0287.7
2.853.2710010.0681.0597.7
2.592.8510010.0971.0367.7
2.412.5910010.1231.0737.7
2.262.4110010.1511.0477.7
2.152.2610010.2061.0257.7
2.062.1510010.2941.0687.4
1.982.0699.410.371.0646.3
1.911.9884.610.4511.084.4
ReflectionResolution: 1.91→50 Å / Num. obs: 74332 / % possible obs: 98.4 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.074 / Χ2: 1.036 / Net I/σ(I): 11.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.91-1.984.40.45163581.08184.6
1.98-2.066.30.3774701.064199.4
2.06-2.157.40.29475021.0681100
2.15-2.267.70.20674931.0251100
2.26-2.417.70.15175521.0471100
2.41-2.597.70.12375041.0731100
2.59-2.857.70.09775511.0361100
2.85-3.277.70.06875781.0591100
3.27-4.117.70.0675811.0281100
4.11-507.60.04977430.912199.9

-
Phasing

PhasingMethod: MAD
Phasing MAD set
IDHighest resolution (Å)Lowest resolution (Å)Power acentricPower centricReflection acentricReflection centric
ISO_11.9145.6600711263134
ISO_21.9145.660.7510.664626182869
ANO_11.9145.661.0230696960
ANO_21.9145.660.620622320
Phasing MAD set shell
IDResolution (Å)Power acentricPower centricReflection acentricReflection centric
ISO_18.41-45.6600768154
ISO_16-8.41001450159
ISO_14.91-6001884157
ISO_14.26-4.91002230157
ISO_13.81-4.26002535157
ISO_13.48-3.81002810153
ISO_13.23-3.48003062164
ISO_13.02-3.23003287154
ISO_12.85-3.02003537159
ISO_12.7-2.85003692157
ISO_12.58-2.7003902152
ISO_12.47-2.58004107162
ISO_12.37-2.47004265157
ISO_12.28-2.37004456155
ISO_12.21-2.28004625162
ISO_12.14-2.21004739149
ISO_12.07-2.14004894159
ISO_12.02-2.07005065151
ISO_11.96-2.02005119164
ISO_11.91-1.96004699152
ANO_18.41-45.661.76907670
ANO_16-8.412.35014500
ANO_14.91-62.206018840
ANO_14.26-4.911.744022300
ANO_13.81-4.261.618025350
ANO_13.48-3.811.631028100
ANO_13.23-3.481.623030610
ANO_13.02-3.231.587032870
ANO_12.85-3.021.463035370
ANO_12.7-2.851.217036920
ANO_12.58-2.71.078039020
ANO_12.47-2.580.921041070
ANO_12.37-2.470.805042650
ANO_12.28-2.370.674044560
ANO_12.21-2.280.556046250
ANO_12.14-2.210.459047390
ANO_12.07-2.140.389048860
ANO_12.02-2.070.33049530
ANO_11.96-2.020.287047110
ANO_11.91-1.960.258037990
ISO_28.41-45.661.9341.419768152
ISO_26-8.411.8751.3171450159
ISO_24.91-61.4921.0711884157
ISO_24.26-4.911.1150.7252230156
ISO_23.81-4.260.9490.6742535157
ISO_23.48-3.810.8750.5732810153
ISO_23.23-3.480.8780.5523062164
ISO_23.02-3.230.8890.583286154
ISO_22.85-3.020.860.5573534159
ISO_22.7-2.850.8220.6113691156
ISO_22.58-2.70.7430.4763901152
ISO_22.47-2.580.6530.4184105162
ISO_22.37-2.470.5630.3884260157
ISO_22.28-2.370.4780.3214450155
ISO_22.21-2.280.4040.3224620162
ISO_22.14-2.210.3370.2524734149
ISO_22.07-2.140.2750.2044888159
ISO_22.02-2.070.2270.1754969151
ISO_21.96-2.020.1970.18144155
ISO_21.91-1.960000
ANO_28.41-45.661.56607670
ANO_26-8.412.188014500
ANO_24.91-62.051018840
ANO_24.26-4.911.664022300
ANO_23.81-4.261.409025350
ANO_23.48-3.811.294028100
ANO_23.23-3.481.193030620
ANO_23.02-3.231.022032860
ANO_22.85-3.020.887035340
ANO_22.7-2.850.71036910
ANO_22.58-2.70.582039000
ANO_22.47-2.580.472041050
ANO_22.37-2.470.389042600
ANO_22.28-2.370.322044500
ANO_22.21-2.280.261046200
ANO_22.14-2.210.224047330
ANO_22.07-2.140.183048580
ANO_22.02-2.070.172047370
ANO_21.96-2.020.16013200
ANO_21.91-1.960000
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
137.28910.98247.389SE28.471.18
257.81525.27479.526SE32.291.34
337.564-0.31425.073SE30.891.39
463.180.02772.856SE32.251.36
535.31118.49524.259SE60.641.05
631.68823.48144.008SE36.010.62
7-42.529-22.262-77.553SE20.30.14
8-57.826-10.882-52.105SE56.140.13
9-40.958-10.788-55.442SE36.010.09
10-37.551-0.609-59.159SE50.610.09
11-21.167-11.049-42.145SE54.340.27
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 74260
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
10.36-10057.70.847508
7.33-10.3648.10.942890
5.98-7.3350.60.9411150
5.18-5.9846.20.9411341
4.63-5.1851.20.951535
4.23-4.6353.70.951669
3.92-4.2350.30.9521818
3.66-3.9253.40.941954
3.45-3.6654.60.942061
3.28-3.4554.30.9262202
3.12-3.28550.922288
2.99-3.1254.20.9122395
2.87-2.9955.70.9132506
2.77-2.8757.10.9132594
2.68-2.7758.50.9092696
2.59-2.6861.40.9052791
2.51-2.5961.50.92849
2.44-2.51630.8972945
2.38-2.4465.50.93036
2.32-2.3867.60.9013105
2.26-2.3270.20.9033191
2.21-2.2672.20.9083257
2.16-2.2173.90.8973327
2.12-2.1676.90.9023383
2.07-2.1277.60.8933488
2.03-2.0780.70.8913545
1.99-2.0382.60.893592
1.96-1.9982.50.8483565
1.91-1.9683.90.7944579

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
DM5phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 1.91→45.64 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.882 / WRfactor Rfree: 0.318 / WRfactor Rwork: 0.266 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.797 / SU R Cruickshank DPI: 0.191 / SU Rfree: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.191 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.301 3745 5 %RANDOM
Rwork0.253 ---
obs0.256 74257 98.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 63.6 Å2 / Biso mean: 21.459 Å2 / Biso min: 5.01 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20.04 Å2
2--0.07 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.91→45.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6090 0 3 437 6530
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0226340
X-RAY DIFFRACTIONr_angle_refined_deg1.5671.9518665
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9015791
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.11422.706303
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.35715932
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0461558
X-RAY DIFFRACTIONr_chiral_restr0.1110.2949
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215011
X-RAY DIFFRACTIONr_mcbond_it0.9471.53953
X-RAY DIFFRACTIONr_mcangle_it1.56526370
X-RAY DIFFRACTIONr_scbond_it2.42332387
X-RAY DIFFRACTIONr_scangle_it3.6434.52295
LS refinement shellResolution: 1.912→1.962 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 268 -
Rwork0.315 4615 -
all-4883 -
obs--88.52 %

+
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