[English] 日本語
Yorodumi
- PDB-4b8w: Crystal structure of human GDP-L-fucose synthase with bound NADP ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4b8w
TitleCrystal structure of human GDP-L-fucose synthase with bound NADP and GDP, tetragonal crystal form
ComponentsGDP-L-FUCOSE SYNTHASE
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


GDP-4-dehydro-D-rhamnose reductase activity / GDP-mannose 3,5-epimerase activity / GDP-fucose biosynthesis / GDP-L-fucose synthase / GDP-L-fucose synthase activity / GDP-mannose metabolic process / positive regulation of endothelial cell-matrix adhesion via fibronectin / 'de novo' GDP-L-fucose biosynthetic process / leukocyte cell-cell adhesion / positive regulation of endothelial cell migration ...GDP-4-dehydro-D-rhamnose reductase activity / GDP-mannose 3,5-epimerase activity / GDP-fucose biosynthesis / GDP-L-fucose synthase / GDP-L-fucose synthase activity / GDP-mannose metabolic process / positive regulation of endothelial cell-matrix adhesion via fibronectin / 'de novo' GDP-L-fucose biosynthetic process / leukocyte cell-cell adhesion / positive regulation of endothelial cell migration / electron transfer activity / extracellular exosome / identical protein binding / cytosol
Similarity search - Function
GDP-L-fucose synthase/GDP-L-colitose synthase / UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / GDP-L-fucose synthase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsVollmar, M. / Krojer, T. / Shafqat, N. / Rojkova, A. / Bunkoczi, G. / Pike, A. / Chaikuat, A. / Carpenter, E. / Yue, W.W. / Kavanagh, K. ...Vollmar, M. / Krojer, T. / Shafqat, N. / Rojkova, A. / Bunkoczi, G. / Pike, A. / Chaikuat, A. / Carpenter, E. / Yue, W.W. / Kavanagh, K. / von Delft, F. / Weigelt, J. / Arrowsmith, C.H. / Bountra, C. / Edwards, A. / Oppermann, U.
CitationJournal: To be Published
Title: Crystal Structure of Human Gdp-L-Fucose Synthase with Bound Nadp and Gdp, Tetragonal Crystal Form
Authors: Vollmar, M. / Krojer, T. / Shafqat, N. / Rojkova, A. / Bunkoczi, G. / Pike, A. / Chaikuat, A. / Carpenter, E. / Yue, W.W. / Kavanagh, K. / von Delft, F. / Weigelt, J. / Arrowsmith, C.H. / ...Authors: Vollmar, M. / Krojer, T. / Shafqat, N. / Rojkova, A. / Bunkoczi, G. / Pike, A. / Chaikuat, A. / Carpenter, E. / Yue, W.W. / Kavanagh, K. / von Delft, F. / Weigelt, J. / Arrowsmith, C.H. / Bountra, C. / Edwards, A. / Oppermann, U.
History
DepositionAug 31, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Structure summary
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GDP-L-FUCOSE SYNTHASE
B: GDP-L-FUCOSE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,1186
Polymers71,7452
Non-polymers2,3734
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6280 Å2
ΔGint-16.9 kcal/mol
Surface area23920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.470, 111.470, 46.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number77
Space group name H-MP42

-
Components

#1: Protein GDP-L-FUCOSE SYNTHASE / GDP-4-KETO-6-DEOXY-D-MANNOSE-3\ / 5-EPIMERASE- 4-REDUCTASE / PROTEIN FX / RED CELL NADP(H)-BINDING ...GDP-4-KETO-6-DEOXY-D-MANNOSE-3\ / 5-EPIMERASE- 4-REDUCTASE / PROTEIN FX / RED CELL NADP(H)-BINDING PROTEIN / SHORT-CHAIN DEHYDROGENASE/REDUCTASE FAMILY 4E MEMBER 1


Mass: 35872.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3 / References: UniProt: Q13630, GDP-L-fucose synthase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsINITIAL RESIDUES NLYFQ DUE TO UNCLEAVED EXPRESSION TAG

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.93 Å3/Da / Density % sol: 36.41 % / Description: NONE
Crystal growDetails: 0.2 M NACL, 0.1 M BIS-TRIS PH 5.5, 25% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9778
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2.75→40.32 Å / Num. obs: 14273 / % possible obs: 93.5 % / Observed criterion σ(I): 1.3 / Redundancy: 3.1 % / Biso Wilson estimate: 79.33 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.2
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 1.3 / % possible all: 93.7

-
Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GFS

1gfs


Resolution: 2.75→40.32 Å / Cor.coef. Fo:Fc: 0.9255 / Cor.coef. Fo:Fc free: 0.8767 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.397
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2524 697 4.88 %RANDOM
Rwork0.201 ---
obs0.2035 14273 93.28 %-
Displacement parametersBiso mean: 69.35 Å2
Baniso -1Baniso -2Baniso -3
1-2.5901 Å20 Å20 Å2
2--2.5901 Å20 Å2
3----5.1802 Å2
Refine analyzeLuzzati coordinate error obs: 0.435 Å
Refinement stepCycle: LAST / Resolution: 2.75→40.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4570 0 152 13 4735
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0084872HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.926696HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2096SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes91HARMONIC2
X-RAY DIFFRACTIONt_gen_planes809HARMONIC5
X-RAY DIFFRACTIONt_it4872HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.24
X-RAY DIFFRACTIONt_other_torsion2.75
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion661SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5591SEMIHARMONIC4
LS refinement shellResolution: 2.75→2.97 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2539 126 4.38 %
Rwork0.2209 2754 -
all0.2224 2880 -
obs--93.28 %
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)
11.5026-0.2003-0.43232.699-0.90622.1538-0.23370.02990.1549-0.0663-0.1465-0.08860.0388-0.270.3801-0.2483-0.00390.0401-0.1525-0.1768-0.030725.623248.03419.8955
22.75971.56371.3864.2614-0.21271.11550.3693-0.2194-0.2860.0377-0.2189-0.05420.5074-0.2179-0.15040.0585-0.18380.157-0.2309-0.0756-0.280927.82319.697112.9622
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

+
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