[English] 日本語
Yorodumi
- PDB-4wac: Crystal Structure of TarM -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4wac
TitleCrystal Structure of TarM
ComponentsGlycosyl transferase, group 1 family protein
KeywordsTRANSFERASE / GT-4 / WTA-specific alpha-O-N-acetylglycosyltransferase / Rossmann fold / DUF1975
Function / homology
Function and homology information


poly(glycerol-phosphate) alpha-glucosyltransferase / poly(glycerol-phosphate) alpha-glucosyltransferase activity / Transferases; Glycosyltransferases / dextransucrase activity / dextransucrase / cytoplasm
Similarity search - Function
Glycosyl transferase, family 1 / Glycosyl transferases group 1 / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / IMIDAZOLE / DI(HYDROXYETHYL)ETHER / Glycosyl transferase family 1 / Glycosyl transferase, group 1 family protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / SIRAS / Resolution: 2.4 Å
AuthorsKoc, C. / Stehle, T. / Xia, G. / Peschel, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation Germany
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structural and Enzymatic Analysis of TarM Glycosyltransferase from Staphylococcus aureus Reveals an Oligomeric Protein Specific for the Glycosylation of Wall Teichoic Acid.
Authors: Koc, C. / Gerlach, D. / Beck, S. / Peschel, A. / Xia, G. / Stehle, T.
History
DepositionAug 29, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Derived calculations
Revision 1.2Apr 22, 2015Group: Database references
Revision 2.0Sep 6, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Derived calculations / Refinement description
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_validate_close_contact / software / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.occupancy / _pdbx_audit_support.funding_organization / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_site_gen.auth_seq_id
Revision 2.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glycosyl transferase, group 1 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3557
Polymers57,9371
Non-polymers4176
Water1,56787
1
A: Glycosyl transferase, group 1 family protein
hetero molecules

A: Glycosyl transferase, group 1 family protein
hetero molecules

A: Glycosyl transferase, group 1 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,06421
Polymers173,8123
Non-polymers1,25218
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area7880 Å2
ΔGint-6 kcal/mol
Surface area67480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.749, 124.749, 223.255
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-686-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Glycosyl transferase, group 1 family protein / TarM


Mass: 57937.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Plasmid: pBAD-TOPO-102a / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10
References: UniProt: Q2FI41, UniProt: A0A0D6HUA0*PLUS, dextransucrase, poly(glycerol-phosphate) alpha-glucosyltransferase

-
Non-polymers , 5 types, 93 molecules

#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 87 / 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: 4.33 Å3/Da / Density % sol: 71.58 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: imidazole, magnesium acetate, PEG 1000 / PH range: 7.7 - 8.2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.07 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionNumber: 1276117 / Rmerge(I) obs: 0.297 / Χ2: 0.95 / D res high: 3.29 Å / D res low: 3.38 Å / Num. obs: 29958 / % possible obs: 99.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obsIDRmerge(I) obs
14.714833410.042
10.414.7161110.045
8.4910.480710.056
7.368.4993610.097
6.587.36106310.149
6.016.58118710.202
5.566.01129010.226
5.25.56136810.22
4.95.2148010.204
4.654.9154210.19
4.444.65162610.191
4.254.44173110.266
4.084.25177410.348
3.934.08183510.513
3.83.93190810.63
3.683.8196210.801
3.573.68206010.905
3.473.57211811.144
3.383.47216811.603
3.293.38215812.191
ReflectionResolution: 2.4→49 Å / Num. obs: 40713 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 9.8 % / Biso Wilson estimate: 47.58 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.119 / Rrim(I) all: 0.126 / Χ2: 0.921 / Net I/σ(I): 14.79 / Num. measured all: 398620
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.4-2.460.5621.5811.6927790295429091.67298.5
2.46-2.530.6861.2782.1127499286928651.35199.9
2.53-2.60.7761.0392.5426211281728121.09999.8
2.6-2.680.8360.8413.2125961270927080.889100
2.68-2.770.8960.6943.9527581267426740.73100
2.77-2.870.9510.5365.0126593254825470.564100
2.87-2.980.9670.4066.4125646247724770.427100
2.98-3.10.980.3068.2424562239623960.322100
3.1-3.240.9880.21611.0823330230022990.228100
3.24-3.390.9940.15414.5821843220022000.162100
3.39-3.580.9960.1071920007210321030.114100
3.58-3.790.9970.08323.3418193200820020.08899.7
3.79-4.060.9980.07226.8817861187618760.076100
4.06-4.380.9990.05533.5118169175917590.058100
4.38-4.80.9990.04737.0916684165316530.049100
4.8-5.370.9990.05134.7514621147814780.054100
5.37-6.20.9990.05532.6712858134613460.058100
6.2-7.590.9980.0534.129661113811320.05399.5
7.59-10.7310.03244.7487159249240.034100
10.730.9980.03247.5348355705530.03497

-
Phasing

PhasingMethod: SIRAS
Phasing MADD res high: 2.9 Å / D res low: 48 Å / FOM acentric: 0.141 / FOM centric: 0.176 / Reflection acentric: 19772 / Reflection centric: 3953
Phasing MAD set
IDHighest resolution (Å)Lowest resolution (Å)Power acentricPower centricReflection acentricReflection centric
ISO_12.94800197703953
ISO_22.9480.6390.605133723051
ANO_12.9480000
ANO_22.9480.2070133720
Phasing MAD set shell
IDResolution (Å)Power acentricPower centricReflection acentricReflection centric
ISO_112.54-4800172186
ISO_19.02-12.5400360195
ISO_17.41-9.0200482204
ISO_16.44-7.4100586195
ISO_15.77-6.4400682198
ISO_15.27-5.7700756198
ISO_14.89-5.2700836197
ISO_14.57-4.8900904202
ISO_14.31-4.5700955195
ISO_14.09-4.31001029202
ISO_13.9-4.09001068186
ISO_13.74-3.9001150205
ISO_13.59-3.74001189203
ISO_13.46-3.59001229196
ISO_13.35-3.46001297200
ISO_13.24-3.35001337205
ISO_13.14-3.24001360188
ISO_13.06-3.14001429203
ISO_12.98-3.06001459190
ISO_12.9-2.98001490205
ANO_112.54-480000
ANO_19.02-12.540000
ANO_17.41-9.020000
ANO_16.44-7.410000
ANO_15.77-6.440000
ANO_15.27-5.770000
ANO_14.89-5.270000
ANO_14.57-4.890000
ANO_14.31-4.570000
ANO_14.09-4.310000
ANO_13.9-4.090000
ANO_13.74-3.90000
ANO_13.59-3.740000
ANO_13.46-3.590000
ANO_13.35-3.460000
ANO_13.24-3.350000
ANO_13.14-3.240000
ANO_13.06-3.140000
ANO_12.98-3.060000
ANO_12.9-2.980000
ISO_212.54-481.6031.106172186
ISO_29.02-12.541.5620.912360195
ISO_27.41-9.021.3940.929482204
ISO_26.44-7.411.3370.892586194
ISO_25.77-6.441.0060.692682198
ISO_25.27-5.770.8390.561756198
ISO_24.89-5.270.6350.392836197
ISO_24.57-4.890.4580.357904202
ISO_24.31-4.570.3880.285955195
ISO_24.09-4.310.320.2541029202
ISO_23.9-4.090.2920.2761068186
ISO_23.74-3.90.2540.211150205
ISO_23.59-3.740.2250.191189203
ISO_23.46-3.590.2020.1741229196
ISO_23.35-3.460.190.141297200
ISO_23.24-3.350.1480.11267790
ISO_23.14-3.240000
ISO_23.06-3.140000
ISO_22.98-3.060000
ISO_22.9-2.980000
ANO_212.54-481.73701720
ANO_29.02-12.541.63903600
ANO_27.41-9.021.32804820
ANO_26.44-7.410.92905860
ANO_25.77-6.440.61306820
ANO_25.27-5.770.46607560
ANO_24.89-5.270.40908360
ANO_24.57-4.890.32809040
ANO_24.31-4.570.23509550
ANO_24.09-4.310.168010290
ANO_23.9-4.090.12010700
ANO_23.74-3.90.085011500
ANO_23.59-3.740.062011890
ANO_23.46-3.590.047012290
ANO_23.35-3.460.042012970
ANO_23.24-3.350.03106750
ANO_23.14-3.240000
ANO_23.06-3.140000
ANO_22.98-3.060000
ANO_22.9-2.980000
Phasing MAD shell
Resolution (Å)FOM acentricFOM centricReflection acentricReflection centric
12.54-480.8090.548172186
9.02-12.540.7250.435360195
7.41-9.020.6080.37482204
6.44-7.410.5270.38586195
5.77-6.440.4060.342682198
5.27-5.770.3580.256756198
4.89-5.270.2850.22836197
4.57-4.890.2260.176904202
4.31-4.570.180.2955195
4.09-4.310.1420.1561029202
3.9-4.090.1090.1461070186
3.74-3.90.0920.1061150205
3.59-3.740.0740.0711189203
3.46-3.590.0590.061229196
3.35-3.460.0480.0591297200
3.24-3.350.0190.0251337205
3.14-3.24001360188
3.06-3.14001429203
2.98-3.06001459190
2.9-2.98001490205

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
SHARPphasing
Cootmodel building
PHENIX(phenix.refine: 1.8.4_1496)refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.4→48.624 Å / FOM work R set: 0.8033 / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2515 2036 5 %
Rwork0.2154 38672 -
obs0.2173 40708 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 226.42 Å2 / Biso mean: 67.56 Å2 / Biso min: 23.59 Å2
Refinement stepCycle: final / Resolution: 2.4→48.624 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4074 0 28 87 4189
Biso mean--63.97 47.57 -
Num. residues----498
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124182
X-RAY DIFFRACTIONf_angle_d1.3265606
X-RAY DIFFRACTIONf_chiral_restr0.056606
X-RAY DIFFRACTIONf_plane_restr0.006718
X-RAY DIFFRACTIONf_dihedral_angle_d15.0431591
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4003-2.45610.34581270.30772413254096
2.4561-2.51750.3491330.284925262659100
2.5175-2.58560.30571330.261325242657100
2.5856-2.66170.3151340.249925442678100
2.6617-2.74760.26611340.236525472681100
2.7476-2.84580.29771340.232625432677100
2.8458-2.95970.30221330.229725462679100
2.9597-3.09440.28471350.220625512686100
3.0944-3.25750.24481350.202225592694100
3.2575-3.46150.25021360.200225972733100
3.4615-3.72870.22811360.190325782714100
3.7287-4.10370.25211360.18525952731100
4.1037-4.69710.20031390.175726362775100
4.6971-5.91630.24091410.218226732814100
5.9163-48.63390.24381500.248428402990100

+
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