[English] 日本語
Yorodumi
- PDB-9vfy: Crystal structure of Phaeodactylibacter sp. phosphoglucomutase in... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9vfy
TitleCrystal structure of Phaeodactylibacter sp. phosphoglucomutase in complex with glucose-6-phosphate
ComponentsPhosphoglucomutase (Alpha-D-glucose-1,6-bisphosphate-dependent)
KeywordsISOMERASE / Metal-binding / Phosphoserine
Function / homology6-O-phosphono-alpha-D-glucopyranose / :
Function and homology information
Biological speciesPhaeodactylibacter sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsShen, Y.W. / Tu, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: In Vitro Design and Optimization of a High-Efficiency Artificial Enzymatic Pathway for Cellulose-to-Starch Conversion
Authors: Shen, Y.W. / Tu, T.
History
DepositionJun 12, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 15, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phosphoglucomutase (Alpha-D-glucose-1,6-bisphosphate-dependent)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4113
Polymers64,1271
Non-polymers2842
Water4,306239
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.904, 59.206, 99.542
Angle α, β, γ (deg.)90.000, 118.048, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-930-

HOH

-
Components

#1: Protein Phosphoglucomutase (Alpha-D-glucose-1,6-bisphosphate-dependent)


Mass: 64126.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phaeodactylibacter sp. (bacteria) / Gene: pgm, KDD09_20305 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A959BHL9, phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent)
#2: Sugar ChemComp-G6P / 6-O-phosphono-alpha-D-glucopyranose / ALPHA-D-GLUCOSE-6-PHOSPHATE / 6-O-phosphono-alpha-D-glucose / 6-O-phosphono-D-glucose / 6-O-phosphono-glucose


Type: D-saccharide, alpha linking / Mass: 260.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13O9P / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
a-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.45 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 0.15 M DL-maleic acid pH 7.0 0.1 M Imidazole pH 6.5 20% v/v polyethylene glycol monomethyl ether 550 3 mM G6P

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97861 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 4, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97861 Å / Relative weight: 1
ReflectionResolution: 1.97→48.06 Å / Num. obs: 37461 / % possible obs: 94 % / Redundancy: 6.7 % / Biso Wilson estimate: 18.91 Å2 / CC1/2: 0.995 / Net I/σ(I): 12.2
Reflection shellResolution: 1.97→2.07 Å / Num. unique obs: 5747 / CC1/2: 0.883

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→48.06 Å / SU ML: 0.205 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 20.4157 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2222 1938 5.18 %
Rwork0.1742 35505 -
obs0.1766 37443 93.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.37 Å2
Refinement stepCycle: LAST / Resolution: 1.97→48.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4181 0 17 239 4437
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00734291
X-RAY DIFFRACTIONf_angle_d0.83255820
X-RAY DIFFRACTIONf_chiral_restr0.0506629
X-RAY DIFFRACTIONf_plane_restr0.005771
X-RAY DIFFRACTIONf_dihedral_angle_d3.23882550
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.020.27771250.22112677X-RAY DIFFRACTION99.12
2.02-2.070.2751690.21082645X-RAY DIFFRACTION99.05
2.07-2.130.23011340.19522646X-RAY DIFFRACTION99.21
2.13-2.20.26281190.18722703X-RAY DIFFRACTION99.3
2.2-2.280.274370.1734764X-RAY DIFFRACTION28.07
2.28-2.370.22821690.17452620X-RAY DIFFRACTION98.45
2.37-2.480.2161820.16612644X-RAY DIFFRACTION99.72
2.48-2.610.23621710.16552637X-RAY DIFFRACTION99.54
2.61-2.770.22481730.16522646X-RAY DIFFRACTION99.37
2.77-2.990.21631180.16322661X-RAY DIFFRACTION97.3
2.99-3.290.21611200.16362723X-RAY DIFFRACTION99.65
3.29-3.760.18051290.15782690X-RAY DIFFRACTION99.3
3.76-4.740.19681580.15552684X-RAY DIFFRACTION98.17
4.74-48.060.2391340.20132765X-RAY DIFFRACTION98.5
Refinement TLS params.Method: refined / Origin x: 10.1355235925 Å / Origin y: -17.5122938934 Å / Origin z: 23.2376423881 Å
111213212223313233
T0.116994867153 Å2-0.00361166288137 Å20.00851907361348 Å2-0.105106939582 Å20.0166646014848 Å2--0.114550324947 Å2
L0.681555667949 °20.289861165867 °20.440696197142 °2-0.617715761607 °20.454385469137 °2--1.07945827634 °2
S-0.0192280823777 Å °0.00955935115822 Å °0.0170751835328 Å °-0.0712682499386 Å °0.0507978086449 Å °-0.10724721901 Å °-0.102605101676 Å °0.0870305517195 Å °-0.0114606754249 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