[English] 日本語
Yorodumi
- PDB-9v0w: UDP-Glc:tetrahydrobiopterin glucosyltransferase from Pseudanabaen... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9v0w
TitleUDP-Glc:tetrahydrobiopterin glucosyltransferase from Pseudanabaena sp. Chao 1811
Componentstetrahydrobiopterin glucosyltransferase
KeywordsTRANSFERASE / UDP-Glc:tetrahydrobiopterin glucosyltransferase
Biological speciesPseudanabaena sp. Chao 1811 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsZang, R.J. / Jiang, Y.L. / Zhou, C.Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32430001 China
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2025
Title: Structural analysis of the tetrahydrobiopterin glucosyltransferase PsBGluT from Pseudanabaena sp. Chao 1811.
Authors: Zang, R. / Jiang, Y. / Zhou, C.Z.
History
DepositionMay 19, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: tetrahydrobiopterin glucosyltransferase
B: tetrahydrobiopterin glucosyltransferase


Theoretical massNumber of molelcules
Total (without water)80,4082
Polymers80,4082
Non-polymers00
Water1,65792
1
A: tetrahydrobiopterin glucosyltransferase

B: tetrahydrobiopterin glucosyltransferase


Theoretical massNumber of molelcules
Total (without water)80,4082
Polymers80,4082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_545x-y,-y-1,-z1
Buried area2100 Å2
ΔGint-12 kcal/mol
Surface area29410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.213, 162.213, 181.952
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

-
Components

#1: Protein tetrahydrobiopterin glucosyltransferase


Mass: 40203.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Sequence reference for Pseudanabaena sp. Chao 1811 (2963092) is not available in UniProt at the time of biocuration. The current reference for the sequence in Uniparc is UPI0022F3A01C.
Source: (gene. exp.) Pseudanabaena sp. Chao 1811 (bacteria) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.3 Å3/Da / Density % sol: 71.38 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: ammonium sulfate 1M, Tris 0.1M pH 8.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54056 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jul 28, 2024 / Details: MMF007 rotating-anode
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54056 Å / Relative weight: 1
ReflectionResolution: 2.8→13.25 Å / Num. obs: 34964 / % possible obs: 99 % / Redundancy: 15 % / Biso Wilson estimate: 51.3 Å2 / Rpim(I) all: 0.044 / Net I/σ(I): 18.3
Reflection shellResolution: 2.8→2.9 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 4609 / Rpim(I) all: 0.576

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487)refinement
CrysalisPro1.171.39.35cdata reduction
Aimless0.8.2data scaling
MOLREP11.9.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→13.25 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2723 1699 4.89 %
Rwork0.2397 --
obs0.2412 34772 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→13.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5548 0 0 92 5640
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065672
X-RAY DIFFRACTIONf_angle_d0.8577707
X-RAY DIFFRACTIONf_dihedral_angle_d13.0972049
X-RAY DIFFRACTIONf_chiral_restr0.054870
X-RAY DIFFRACTIONf_plane_restr0.007989
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.880.36161430.32652693X-RAY DIFFRACTION100
2.88-2.970.40391430.32312716X-RAY DIFFRACTION100
2.97-3.080.32641640.32262694X-RAY DIFFRACTION100
3.08-3.20.34051290.32672740X-RAY DIFFRACTION100
3.2-3.340.35271280.30132745X-RAY DIFFRACTION100
3.34-3.520.31641450.28992736X-RAY DIFFRACTION100
3.52-3.730.32211290.26922739X-RAY DIFFRACTION99
3.73-4.010.29451320.25952733X-RAY DIFFRACTION99
4.01-4.40.21491230.20952762X-RAY DIFFRACTION99
4.4-5.010.22481470.19742768X-RAY DIFFRACTION99
5.01-6.20.25351590.20862822X-RAY DIFFRACTION100
6.2-13.250.20561570.1752925X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -11.2377 Å / Origin y: -58.4369 Å / Origin z: 12.463 Å
111213212223313233
T0.3426 Å20.0411 Å2-0.1329 Å2-0.7426 Å2-0.2433 Å2--0.5699 Å2
L0.5432 °2-0.0531 °2-0.15 °2-0.3963 °20.4078 °2--0.5208 °2
S0.0505 Å °0.365 Å °-0.2218 Å °-0.1612 Å °0.1987 Å °-0.2827 Å °-0.0378 Å °0.2842 Å °-0.0891 Å °
Refinement TLS groupSelection details: all

+
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