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- PDB-4b8z: Crystal structure of human GDP-L-fucose synthase with bound NADP ... -

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Basic information

Entry
Database: PDB / ID: 4b8z
TitleCrystal structure of human GDP-L-fucose synthase with bound NADP and GDP, rhombohedral 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-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
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. / Yue, W.W. / Kavanagh, K. / von Delft, F. / Weigelt, J. / Arrowsmith, C.H. ...Vollmar, M. / Krojer, T. / Shafqat, N. / Rojkova, A. / Bunkoczi, G. / 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, Rhombohedral Crystal Form
Authors: Vollmar, M. / Krojer, T. / Shafqat, N. / Rojkova, A. / Bunkoczi, G. / 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 1.0Feb 6, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2Jun 20, 2018Group: Data collection / Derived calculations / Category: struct_conn
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)148,75312
Polymers144,0064
Non-polymers4,7468
Water32418
1
A: GDP-L-FUCOSE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1883
Polymers36,0021
Non-polymers1,1872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GDP-L-FUCOSE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1883
Polymers36,0021
Non-polymers1,1872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: GDP-L-FUCOSE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1883
Polymers36,0021
Non-polymers1,1872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: GDP-L-FUCOSE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1883
Polymers36,0021
Non-polymers1,1872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.447, 91.447, 429.130
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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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: 36001.602 Da / Num. of mol.: 4 / Fragment: RESIDUES 7-320
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.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.8 % / Description: NONE
Crystal growDetails: 0.3M NABR, 0.1M BIS-TRIS-PROPANE (PH 7.5), 23% PEG3350, 10% ETHYLENE GLYCOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9792
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.75→77.88 Å / Num. obs: 34584 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 92.48 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.8
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2 / % possible all: 100

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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→77.88 Å / Cor.coef. Fo:Fc: 0.9201 / Cor.coef. Fo:Fc free: 0.8928 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.358
RfactorNum. reflection% reflectionSelection details
Rfree0.261 1742 5.04 %RANDOM
Rwork0.2333 ---
obs0.2347 34583 99.31 %-
Displacement parametersBiso mean: 83.08 Å2
Baniso -1Baniso -2Baniso -3
1-3.3085 Å20 Å20 Å2
2--3.3085 Å20 Å2
3----6.617 Å2
Refine analyzeLuzzati coordinate error obs: 0.521 Å
Refinement stepCycle: LAST / Resolution: 2.75→77.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9170 0 304 18 9492
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0089746HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9113388HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4172SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes187HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1624HARMONIC5
X-RAY DIFFRACTIONt_it9746HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.27
X-RAY DIFFRACTIONt_other_torsion2.68
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1342SEMIHARMONIC5
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_contact10828SEMIHARMONIC4
LS refinement shellResolution: 2.75→2.83 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.2828 175 5.76 %
Rwork0.264 2861 -
all0.2651 3036 -
obs--99.31 %
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)
11.71120.1548-0.95252.98350.34032.1753-0.00340.36310.1995-0.87150.0791-0.6154-0.20420.3087-0.0757-0.0252-0.02360.2618-0.20390.0538-0.209725.6084.8845-21.2025
23.47410.21130.592.06110.41051.6786-0.00350.3702-0.2089-0.13420.1069-0.07190.16390.1833-0.1035-0.2023-0.07090.0304-0.1168-0.0055-0.117332.47763.928-94.677
32.4407-0.26120.31273.24060.75382.1610.1465-0.26380.14310.3309-0.0028-0.1941-0.00790.2717-0.1437-0.1357-0.087-0.0324-0.22910.0445-0.113112.313922.96319.2397
41.30540.2871-0.67143.9792-0.12721.78250.0531-0.26620.17961.0492-0.04080.7582-0.222-0.2162-0.01230.0571-0.0560.2699-0.2633-0.0161-0.226119.861231.4494-63.7274
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D

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