[English] 日本語
Yorodumi
- PDB-3pnn: The crystal structure of a glycosyltransferase from Porphyromonas... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3pnn
TitleThe crystal structure of a glycosyltransferase from Porphyromonas gingivalis W83
ComponentsConserved domain proteinProtein domain
KeywordsTRANSFERASE / structural genomics / PSI-Biology / protein structure initiative / midwest center for structural genomics / MCSG / alpha/beta/alpha Rossmann fold-like / formation of the glycosidic linkage / cytoplasmic
Function / homologySpore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta / Conserved domain protein
Function and homology information
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.901 Å
AuthorsTan, K. / Hatzos-Skintges, C. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a glycosyltransferase from Porphyromonas gingivalis W83
Authors: Tan, K. / Hatzos-Skintges, C. / Bearden, J. / Joachimiak, A.
History
DepositionNov 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 8, 2012Group: Other

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Conserved domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8667
Polymers34,3141
Non-polymers5536
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)109.038, 109.038, 124.637
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-326-

HOH

DetailsExperimentally unknown. It is predicted that the molecule is monomeric.

-
Components

#1: Protein Conserved domain protein / Protein domain / glycosyltransferase


Mass: 34313.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Strain: W83 / Gene: PG_0160 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q7MXL4
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 3.12 Å3/Da / Density % sol: 60.53 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1M Sodium Citrate Tribasic, 0.1M Sodium Cacodylate:HCl, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97942 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 13, 2010 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 1.9→44.2 Å / Num. all: 34856 / Num. obs: 34856 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.7 % / Biso Wilson estimate: 30.71 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 43.9
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 11.9 % / Rmerge(I) obs: 0.649 / Mean I/σ(I) obs: 4.1 / Num. unique all: 1711 / % possible all: 100

-
Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.901→44.153 Å / SU ML: 0.14 / σ(F): 0.01 / σ(I): 0 / Phase error: 17.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1834 1684 5.01 %random
Rwork0.1658 ---
obs0.1667 33637 96.11 %-
all-33637 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.466 Å2 / ksol: 0.367 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.6781 Å20 Å20 Å2
2---3.6781 Å2-0 Å2
3---7.3563 Å2
Refinement stepCycle: LAST / Resolution: 1.901→44.153 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2374 0 36 203 2613
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082510
X-RAY DIFFRACTIONf_angle_d1.0783386
X-RAY DIFFRACTIONf_dihedral_angle_d17.039937
X-RAY DIFFRACTIONf_chiral_restr0.073357
X-RAY DIFFRACTIONf_plane_restr0.005442
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9007-1.96860.2221450.18012804X-RAY DIFFRACTION86
1.9686-2.04750.2041410.16733059X-RAY DIFFRACTION93
2.0475-2.14070.19421540.16323070X-RAY DIFFRACTION94
2.1407-2.25350.18611750.16343130X-RAY DIFFRACTION96
2.2535-2.39470.18941800.16393195X-RAY DIFFRACTION97
2.3947-2.57960.19751960.17043186X-RAY DIFFRACTION98
2.5796-2.83910.18661500.17983293X-RAY DIFFRACTION99
2.8391-3.24980.18651890.17333314X-RAY DIFFRACTION99
3.2498-4.0940.17051860.15353352X-RAY DIFFRACTION99
4.094-44.16480.17381680.16273550X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -10.0518 Å / Origin y: 34.9385 Å / Origin z: 13.3354 Å
111213212223313233
T0.2512 Å20.006 Å20.0063 Å2-0.2265 Å2-0.01 Å2--0.2662 Å2
L1.8264 °2-0.1165 °2-0.1852 °2-0.4333 °2-0.2768 °2--0.9893 °2
S-0 Å °0.0494 Å °-0.2592 Å °-0.0669 Å °-0.0156 Å °-0.0016 Å °0.1216 Å °0.017 Å °0.0168 Å °
Refinement TLS groupSelection details: chain A

+
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