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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4bkp
TitleCrystal structure of human GDP-L-fucose synthase with bound NADP
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-mannose metabolic process / GDP-L-fucose synthase activity / 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-mannose metabolic process / GDP-L-fucose synthase activity / 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
CITRATE ANION / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / GDP-L-fucose synthase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsVollmar, M. / Shafqat, N. / Rojkova, A. / Krojer, T. / Bradley, A. / Raynor, J.W. / Kavanagh, K. / von Delft, F. / Arrowsmith, C.H. / Bountra, C. ...Vollmar, M. / Shafqat, N. / Rojkova, A. / Krojer, T. / Bradley, A. / Raynor, J.W. / Kavanagh, K. / von Delft, F. / Arrowsmith, C.H. / Bountra, C. / Edwards, A. / Oppermann, U. / Yue, W.W.
CitationJournal: To be Published
Title: Crystal Structure of Human Gdp-L-Fucose Synthase with Bound Nadp
Authors: Vollmar, M. / Shafqat, N. / Rojkova, A. / Krojer, T. / Bradley, A. / Raynor, J.W. / Kavanagh, K. / von Delft, F. / Arrowsmith, C.H. / Bountra, C. / Edwards, A. / Oppermann, U. / Yue, W.W.
History
DepositionApr 29, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2Dec 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
C: GDP-L-FUCOSE SYNTHASE
D: GDP-L-FUCOSE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,45510
Polymers151,2304
Non-polymers3,2256
Water90150
1
A: GDP-L-FUCOSE SYNTHASE
B: GDP-L-FUCOSE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,2915
Polymers75,6152
Non-polymers1,6763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-23.6 kcal/mol
Surface area27240 Å2
MethodPISA
2
C: GDP-L-FUCOSE SYNTHASE
D: GDP-L-FUCOSE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,1645
Polymers75,6152
Non-polymers1,5493
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-22.5 kcal/mol
Surface area26480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.596, 163.095, 197.581
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

-
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: 37807.586 Da / Num. of mol.: 4
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 / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.82 % / Description: NONE
Crystal growDetails: 20% PEG 3350, 0.1M CITRATE PH 5.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.7→49.4 Å / Num. obs: 47605 / % possible obs: 100 % / Observed criterion σ(I): 1.9 / Redundancy: 6.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.9
Reflection shellResolution: 2.7→2.79 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.07 / Mean I/σ(I) obs: 1.9 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4B8W

4b8w


Resolution: 2.7→49.44 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.934 / SU B: 22.103 / SU ML: 0.223 / Cross valid method: THROUGHOUT / ESU R: 0.766 / ESU R Free: 0.299 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.23091 2408 5.1 %RANDOM
Rwork0.19603 ---
obs0.1978 45196 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.195 Å2
Baniso -1Baniso -2Baniso -3
1-0.94 Å20 Å20 Å2
2--0.47 Å20 Å2
3----1.4 Å2
Refinement stepCycle: LAST / Resolution: 2.7→49.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9797 0 209 50 10056
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01910274
X-RAY DIFFRACTIONr_bond_other_d0.0030.029116
X-RAY DIFFRACTIONr_angle_refined_deg1.1981.9514057
X-RAY DIFFRACTIONr_angle_other_deg0.868320799
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.22851290
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.98924.044455
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.524151413
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9041542
X-RAY DIFFRACTIONr_chiral_restr0.0620.21567
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02111894
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022540
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.0448.8385172
X-RAY DIFFRACTIONr_mcbond_other5.0428.8385171
X-RAY DIFFRACTIONr_mcangle_it7.21516.5826458
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.0989.1195100
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 169 -
Rwork0.332 3334 -
obs--99.94 %
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)
10.44660.27070.35110.41841.07833.26030.1105-0.0929-0.05940.0716-0.1719-0.00130.097-0.37570.06140.1213-0.0254-0.02510.2293-0.04790.0864-3.3488-17.2929-53.5008
22.1161.02260.15361.0036-0.02460.74010.1956-0.0124-0.2851-0.0785-0.1355-0.18570.1103-0.1182-0.060.2136-0.0102-0.04940.2157-0.07760.1436-0.9069-28.9014-66.1789
32.9011.85821.06131.44020.44721.83910.5876-0.3596-0.37730.3676-0.3565-0.24250.4512-0.194-0.23110.223-0.0967-0.14670.14210.03680.1407-6.6841-38.7305-56.8707
40.4866-0.21561.20240.4490.14974.5726-0.08920.08360.0951-0.05990.0747-0.179-0.3580.12130.01450.235-0.10780.0290.3482-0.06540.07714.0726-10.1301-94.4036
51.2160.5815-1.16350.4314-0.46941.2776-0.16330.0593-0.2459-0.05160.0435-0.20390.04250.09190.11980.2142-0.02760.01460.305-0.15080.176420.2234-20.857-81.52
65.42740.96950.0841.751-0.3321.9518-0.23440.6701-0.5816-0.21710.214-0.49320.32790.42580.02040.0939-0.01280.09980.3551-0.25630.29430.8288-23.5959-91.9697
71.14820.4075-0.60040.355-0.20083.9601-0.17740.2375-0.322-0.14430.0335-0.08230.225-0.00570.14390.0973-0.00110.06770.0706-0.05650.166-18.1041-2.5073-45.0844
81.33150.31840.40091.60320.78680.5532-0.0867-0.026-0.147-0.101-0.03580.0623-0.0446-0.03060.12250.085-0.01720.01660.13850.02980.1563-26.42884.7865-32.1299
93.04830.8417-0.58833.0242-0.48491.2217-0.37470.568-0.6873-0.1890.21470.1161-0.046-0.3790.160.0851-0.05230.02490.1785-0.11290.276-40.4248-7.0248-40.2757
100.4345-0.7430.6071.9021-1.69851.5435-0.18070.0204-0.05930.7237-0.2974-0.3821-0.64210.3310.4780.7738-0.1799-0.19660.23580.17740.4133-11.15915.90092.7143
111.0420.7930.65743.2653-1.22025.51310.17-0.0641-0.19940.1185-0.031-0.4639-0.09220.2121-0.1390.0997-0.0146-0.06430.11850.0370.1423-9.084613.5718-15.7318
121.2460.42281.00392.78670.64231.7551-0.1875-0.29310.18020.4394-0.1268-0.0352-0.2928-0.28450.31430.26970.0732-0.08960.1171-0.02760.0794-20.625226.9152-11.3509
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-11 - 80
2X-RAY DIFFRACTION2A81 - 208
3X-RAY DIFFRACTION3A209 - 320
4X-RAY DIFFRACTION4B-11 - 78
5X-RAY DIFFRACTION5B79 - 210
6X-RAY DIFFRACTION6B211 - 320
7X-RAY DIFFRACTION7C-12 - 78
8X-RAY DIFFRACTION8C79 - 183
9X-RAY DIFFRACTION9C184 - 321
10X-RAY DIFFRACTION10D-7 - 35
11X-RAY DIFFRACTION11D36 - 92
12X-RAY DIFFRACTION12D93 - 320

+
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