[English] 日本語
Yorodumi
- PDB-8du0: Crystal Structure of NADP bound GDP-L-fucose synthase from Brucel... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8du0
TitleCrystal Structure of NADP bound GDP-L-fucose synthase from Brucella ovis
ComponentsGDP-L-fucose synthase
KeywordsISOMERASE / SSGCID / Multifunctional enzyme / Oxidoreductase / NADP / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


GDP-L-fucose synthase / GDP-L-fucose synthase activity / 'de novo' GDP-L-fucose biosynthetic process / NADP+ binding / isomerase activity
Similarity search - Function
GDP-L-fucose synthase/GDP-L-colitose synthase / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / GDP-L-fucose synthase
Similarity search - Component
Biological speciesBrucella ovis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: to be published
Title: Crystal Structure of NADP bound GDP-L-fucose synthase from Brucella ovis
Authors: DeBouver, N.D. / Davies, D.R. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionJul 26, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GDP-L-fucose synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7333
Polymers36,8981
Non-polymers8352
Water1,11762
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.820, 75.820, 112.530
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-533-

HOH

-
Components

#1: Protein GDP-L-fucose synthase / GDP-4-keto-6-deoxy-D-mannose-3 / 5-epimerase-4-reductase


Mass: 36897.914 Da / Num. of mol.: 1 / Fragment: BrovA.00085.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella ovis (bacteria) / Strain: ATCC 25840 / 63/290 / NCTC 10512 / Gene: fcl, BOV_A0361 / Plasmid: BrovA.00085.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3AU93, GDP-L-fucose synthase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.39 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: [Target: BrovA.00085.a.B1.PS02318 - 20 mg/mL] [Barcode: 324698e1] [Pin: dnq8-5] [Crystallization: optimization screen based on MCSG1 h6 - 0.1M Sodium acetate/HCl pH 4.6, 3.5M Sodium formate, ...Details: [Target: BrovA.00085.a.B1.PS02318 - 20 mg/mL] [Barcode: 324698e1] [Pin: dnq8-5] [Crystallization: optimization screen based on MCSG1 h6 - 0.1M Sodium acetate/HCl pH 4.6, 3.5M Sodium formate, 14C, 0.2:0.2 drop ratio] [Cryo: direct]

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 23, 2022 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.1→32.83 Å / Num. obs: 22404 / % possible obs: 99.9 % / Redundancy: 4.866 % / Biso Wilson estimate: 48.6 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.048 / Rrim(I) all: 0.054 / Χ2: 0.924 / Net I/σ(I): 16.65 / Num. measured all: 109014
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.1-2.154.9210.542.868046163516350.9050.606100
2.15-2.214.9410.4193.587886159615960.9290.47100
2.21-2.284.9260.334.517616154615460.950.37100
2.28-2.354.9260.2465.967399150215020.9710.276100
2.35-2.424.9220.197.517196146214620.980.213100
2.42-2.514.9470.1419.367030142114210.990.158100
2.51-2.64.9350.11211.176712136013600.9940.125100
2.6-2.714.9270.09613.136484131613160.9950.108100
2.71-2.834.9410.07615.876250126712650.9960.08699.8
2.83-2.974.8960.05719.865900120512050.9980.064100
2.97-3.134.8960.0522.635650115511540.9980.05699.9
3.13-3.324.8850.04525.835388110411030.9980.0599.9
3.32-3.554.840.04229.915005103410340.9980.047100
3.55-3.834.8420.0431.1246779669660.9980.045100
3.83-4.24.8020.03933.3143229019000.9980.04499.9
4.2-4.74.7770.03634.5739418258250.9980.041100
4.7-5.424.7330.03834.4534037207190.9980.04399.9
5.42-6.644.6210.03934.1528426156150.9970.044100
6.64-9.394.4420.0434.2622215015000.9970.04699.8
9.39-32.833.7360.04232.1610462962800.9940.04994.6

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.20-4487refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold2

Resolution: 2.1→32.83 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2434 2115 9.44 %
Rwork0.206 20279 -
obs0.2093 22394 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 154.94 Å2 / Biso mean: 75.0959 Å2 / Biso min: 35.54 Å2
Refinement stepCycle: final / Resolution: 2.1→32.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2089 0 54 62 2205
Biso mean--56.68 62.49 -
Num. residues----286
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.150.32041580.279213111469100
2.15-2.20.28171660.266412921458100
2.2-2.260.26251370.249513361473100
2.26-2.330.28951500.23413321482100
2.33-2.40.28111250.221513211446100
2.4-2.490.26721620.220913101472100
2.49-2.590.28611350.216913581493100
2.59-2.710.29561270.243413721499100
2.71-2.850.28981370.258413261463100
2.85-3.030.28531250.23113681493100
3.03-3.260.28131360.227813541490100
3.26-3.590.23541480.220613541502100
3.59-4.110.25161260.180713991525100
4.11-5.170.20161420.173613701512100
5.17-32.830.20721410.19071476161799
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.3076-0.8027-0.5882.25210.28712.5806-0.30231.3118-0.4038-0.3824-0.2277-0.21081.0451-0.2059-0.41950.73430.00550.07161.2972-0.52710.467120.288116.1992-21.6373
21.5661-1.39-0.86892.43580.33270.6495-0.10771.8474-0.7313-1.0337-0.24620.43890.868-0.44460.42690.8793-0.08720.04541.4214-0.54650.796914.00213.4411-20.3411
33.5062-0.5506-0.40493.4760.17483.8808-0.19750.991-0.34560.0334-0.08420.08860.4845-0.21370.27030.2967-0.06270.07450.6358-0.10410.423116.029424.4387-9.2184
42.36850.08740.15472.03470.13934.5781-0.29861.04760.25770.014-0.0861-0.3480.24990.11420.30270.218-0.02830.06790.6290.00920.428521.132529.112-8.6835
52.64693.19421.07314.00071.33770.4429-0.50181.41231.52-0.5386-0.04840.43180.02721.02950.29640.5309-0.0310.02581.68710.41650.94094.840539.7452-30.534
64.13520.04352.93151.4522-0.5683.22270.04141.6670.71-0.3161-0.3686-0.30490.07670.4515-0.16070.42460.07910.12721.37080.13310.528825.415628.6401-21.7538
73.59610.34860.47741.2656-0.70110.55740.03392.20282.2612-0.4563-0.4228-0.5883-0.3030.32640.95170.4254-0.0261-0.00831.77830.78821.359320.733843.309-28.9422
82.50880.63742.56471.69011.50163.1442-0.55581.60591.1072-0.6179-0.10730.1594-0.58020.22060.01580.5715-0.14040.00591.71530.61760.901617.525743.4674-30.5953
92.9321-1.26841.62880.8435-0.6680.92850.24031.92590.6644-0.8592-0.4683-0.5101-0.0255-0.190.12640.7260.11140.08812.20080.3640.641621.963132.4446-30.7306
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 19 through 43 )A19 - 43
2X-RAY DIFFRACTION2chain 'A' and (resid 44 through 63 )A44 - 63
3X-RAY DIFFRACTION3chain 'A' and (resid 64 through 144 )A64 - 144
4X-RAY DIFFRACTION4chain 'A' and (resid 145 through 191 )A145 - 191
5X-RAY DIFFRACTION5chain 'A' and (resid 192 through 215 )A192 - 215
6X-RAY DIFFRACTION6chain 'A' and (resid 216 through 256 )A216 - 256
7X-RAY DIFFRACTION7chain 'A' and (resid 257 through 271 )A257 - 271
8X-RAY DIFFRACTION8chain 'A' and (resid 272 through 299 )A272 - 299
9X-RAY DIFFRACTION9chain 'A' and (resid 300 through 327 )A300 - 327

+
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://pdbjlvh1.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