[English] 日本語
Yorodumi
- PDB-9fjz: Teth514_1788 1,2-beta-oligomannan phosphorylase in complex with m... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9fjz
TitleTeth514_1788 1,2-beta-oligomannan phosphorylase in complex with mannoheptaose
Components1,2-beta-oligomannan phosphorylase
KeywordsCYTOSOLIC PROTEIN / Enzyme / Phosphorylase / Carbohydrate / Mannose
Function / homology1,2-beta-oligomannan phosphorylase / Mannoside phosphorylase / beta-1,4-mannooligosaccharide phosphorylase / GDP-mannose biosynthetic process / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / glycosyltransferase activity / PHOSPHATE ION / 1,2-beta-oligomannan phosphorylase
Function and homology information
Biological speciesThermoanaerobacter sp. X514 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsCioci, G. / Ladeveze, S. / Durand, J. / Potocki-Veronese, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Teth514_1788 1,2-beta-oligomannan phosphorylase in complex with mannopentaose
Authors: Cioci, G. / Ladeveze, S. / Durand, J. / Potocki-Veronese, G.
History
DepositionMay 31, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 1,2-beta-oligomannan phosphorylase
B: 1,2-beta-oligomannan phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,56212
Polymers69,8562
Non-polymers2,70610
Water9,278515
1
A: 1,2-beta-oligomannan phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2627
Polymers34,9281
Non-polymers1,3346
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 1,2-beta-oligomannan phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3005
Polymers34,9281
Non-polymers1,3724
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)137.110, 137.110, 168.638
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: HIS / End label comp-ID: HIS / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 2 - 299 / Label seq-ID: 2 - 299

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein 1,2-beta-oligomannan phosphorylase / 1 / 2-beta-oligomannan:phosphate alpha-D-mannosyltransferase


Mass: 34927.945 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacter sp. X514 (bacteria) / Gene: Teth514_1788 / Production host: Escherichia coli (E. coli)
References: UniProt: B0K2C2, 1,2-beta-oligomannan phosphorylase

-
Sugars , 2 types, 2 molecules

#2: Polysaccharide beta-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-2)-beta-D- ...beta-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-2)-beta-D-mannopyranose


Type: oligosaccharide / Mass: 990.860 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-2DManpb1-2DManpb1-2DManpb1-2DManpb1-2DManpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,6,5/[a1122h-1b_1-5]/1-1-1-1-1-1/a2-b1_b2-c1_c2-d1_d2-e1_e2-f1WURCSPDB2Glycan 1.1.0
[][b-D-Manp]{[(2+1)][b-D-Manp]{[(2+1)][b-D-Manp]{[(2+1)][b-D-Manp]{[(2+1)][b-D-Manp]{[(2+1)][b-D-Manp]{}}}}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-2)-beta-D- ...beta-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-2)-beta-D-mannopyranose


Type: oligosaccharide / Mass: 1153.001 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DManpb1-2DManpb1-2DManpb1-2DManpb1-2DManpb1-2DManpb1-2DManpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,7,6/[a1122h-1b_1-5]/1-1-1-1-1-1-1/a2-b1_b2-c1_c2-d1_d2-e1_e2-f1_f2-g1WURCSPDB2Glycan 1.1.0
[][b-D-Manp]{[(2+1)][b-D-Manp]{[(2+1)][b-D-Manp]{[(2+1)][b-D-Manp]{[(2+1)][b-D-Manp]{[(2+1)][b-D-Manp]{[(2+1)][b-D-Manp]{}}}}}}}LINUCSPDB-CARE

-
Non-polymers , 3 types, 523 molecules

#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 515 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 6.55 Å3/Da / Density % sol: 81.22 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.8M Na Citrate 0.1M Na Cacodylater pH 6.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 81687 / % possible obs: 100 % / Redundancy: 7.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.09 / Net I/σ(I): 6.5
Reflection shellResolution: 2.3→2.42 Å / Rmerge(I) obs: 0.734 / Num. unique obs: 11816 / CC1/2: 0.83

-
Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→44.92 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.964 / SU B: 3.292 / SU ML: 0.076 / Cross valid method: FREE R-VALUE / ESU R: 0.124 / ESU R Free: 0.109
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1751 4081 4.997 %
Rwork0.1683 77581 -
all0.169 --
obs-81662 99.917 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 39.083 Å2
Baniso -1Baniso -2Baniso -3
1-0.177 Å20.089 Å20 Å2
2--0.177 Å2-0 Å2
3----0.576 Å2
Refinement stepCycle: LAST / Resolution: 2.3→44.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4814 0 179 515 5508
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0125124
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164791
X-RAY DIFFRACTIONr_angle_refined_deg0.8711.8386956
X-RAY DIFFRACTIONr_angle_other_deg0.3761.77511098
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9995594
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.313530
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.74510848
X-RAY DIFFRACTIONr_dihedral_angle_6_deg11.01710234
X-RAY DIFFRACTIONr_chiral_restr0.040.2771
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025796
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021128
X-RAY DIFFRACTIONr_nbd_refined0.1690.2719
X-RAY DIFFRACTIONr_symmetry_nbd_other0.210.24546
X-RAY DIFFRACTIONr_nbtor_refined0.1720.22355
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.22328
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1090.2459
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1170.213
X-RAY DIFFRACTIONr_nbd_other0.0990.242
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.140.215
X-RAY DIFFRACTIONr_mcbond_it1.2484.0452382
X-RAY DIFFRACTIONr_mcbond_other1.2484.0452382
X-RAY DIFFRACTIONr_mcangle_it2.147.2652974
X-RAY DIFFRACTIONr_mcangle_other2.147.2682975
X-RAY DIFFRACTIONr_scbond_it1.784.5892742
X-RAY DIFFRACTIONr_scbond_other1.784.5882743
X-RAY DIFFRACTIONr_scangle_it3.1468.3593982
X-RAY DIFFRACTIONr_scangle_other3.1458.3583983
X-RAY DIFFRACTIONr_lrange_it5.9743.0915552
X-RAY DIFFRACTIONr_lrange_other5.86641.9445417
X-RAY DIFFRACTIONr_ncsr_local_group_10.0460.0510187
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.045820.05011
12AX-RAY DIFFRACTIONLocal ncs0.045820.05011
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.3-2.360.263160.26656440.26559620.9570.96299.96650.244
2.36-2.4240.2782630.25155660.25258290.9630.9661000.228
2.424-2.4940.2672960.2353800.23256770.9630.9799.98240.207
2.494-2.5710.2542800.22451760.22554580.9630.9799.96340.2
2.571-2.6550.2333160.20450240.20553410.9680.97499.98130.184
2.655-2.7480.2152350.19749460.19751830.9730.97799.96140.178
2.748-2.8510.212530.18747330.18849870.9730.97999.97990.171
2.851-2.9670.1832490.17545830.17548330.9790.98199.97930.162
2.967-3.0980.1782270.17343680.17345960.980.98299.97820.163
3.098-3.2480.1941930.17942450.1844400.9810.98299.9550.171
3.248-3.4230.1562320.1839640.17941980.9870.98499.95240.175
3.423-3.630.1772200.17337700.17339930.9840.98599.92490.171
3.63-3.8780.1631670.15736080.15737770.9860.98799.9470.156
3.878-4.1860.1321610.14233340.14134990.9880.98899.88570.143
4.186-4.5820.131610.12831000.12832620.9890.9999.96930.131
4.582-5.1160.1081420.11828010.11729510.9930.99399.72890.121
5.116-5.8950.1721190.14624880.14826150.9870.9999.69410.149
5.895-7.1890.1611210.15621220.15622450.9850.98799.91090.156
7.189-10.0390.177900.15116920.15217870.9820.98799.72020.154
10.039-44.920.139400.1710370.16910810.990.9899.630.179

+
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