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- PDB-4bl5: Crystal structure of human GDP-L-fucose synthase with bound NADP ... -

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Basic information

Entry
Database: PDB / ID: 4bl5
TitleCrystal structure of human GDP-L-fucose synthase with bound NADP and product GDP-L-fucose
ComponentsGDP-L-FUCOSE SYNTHASE
KeywordsOXIDOREDUCTASE / ISOMERASE
Function / homology
Function and homology information


GDP-4-dehydro-D-rhamnose reductase activity / GDP-mannose 3,5-epimerase activity / positive regulation of endothelial cell-matrix adhesion via fibronectin / GDP-fucose biosynthesis / GDP-L-fucose synthase / GDP-L-fucose synthase activity / GDP-mannose metabolic process / '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 / positive regulation of endothelial cell-matrix adhesion via fibronectin / GDP-fucose biosynthesis / GDP-L-fucose synthase / GDP-L-fucose synthase activity / GDP-mannose metabolic process / '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-BETA-L-FUCOPYRANOSE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / GDP-L-fucose synthase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 and Product Gdp-L-Fucose
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
DepositionMay 1, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 21, 2014Provider: 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _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

Downloads & links

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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
E: GDP-L-FUCOSE SYNTHASE
F: GDP-L-FUCOSE SYNTHASE
G: GDP-L-FUCOSE SYNTHASE
H: GDP-L-FUCOSE SYNTHASE
I: GDP-L-FUCOSE SYNTHASE
J: GDP-L-FUCOSE SYNTHASE
K: GDP-L-FUCOSE SYNTHASE
L: GDP-L-FUCOSE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)469,74637
Polymers453,69112
Non-polymers16,05525
Water73941
1
H: GDP-L-FUCOSE SYNTHASE
I: GDP-L-FUCOSE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,2816
Polymers75,6152
Non-polymers2,6654
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-28.1 kcal/mol
Surface area23600 Å2
MethodPISA
2
G: GDP-L-FUCOSE SYNTHASE
J: GDP-L-FUCOSE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,2816
Polymers75,6152
Non-polymers2,6654
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-26.9 kcal/mol
Surface area23370 Å2
MethodPISA
3
A: GDP-L-FUCOSE SYNTHASE
E: GDP-L-FUCOSE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,2816
Polymers75,6152
Non-polymers2,6654
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-26.8 kcal/mol
Surface area23500 Å2
MethodPISA
4
B: GDP-L-FUCOSE SYNTHASE
D: GDP-L-FUCOSE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,2816
Polymers75,6152
Non-polymers2,6654
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-27 kcal/mol
Surface area22920 Å2
MethodPISA
5
K: GDP-L-FUCOSE SYNTHASE
L: GDP-L-FUCOSE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,2816
Polymers75,6152
Non-polymers2,6654
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-24.6 kcal/mol
Surface area23300 Å2
MethodPISA
6
C: GDP-L-FUCOSE SYNTHASE
F: GDP-L-FUCOSE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,3437
Polymers75,6152
Non-polymers2,7285
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-23.3 kcal/mol
Surface area23430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.407, 90.478, 147.518
Angle α, β, γ (deg.)72.54, 72.64, 60.14
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: NAP / Beg label comp-ID: NAP / End auth comp-ID: GFB / End label comp-ID: GFB / Refine code: 1 / Auth seq-ID: 901 - 902

Dom-IDAuth asym-IDLabel asym-ID
1AM - N
2BO - P
3CQ - R
4DS - T
5EU - V
6FW - X
7GZ - AA
8HBA - CA
9IDA - EA
10JFA - GA
11KHA - IA
12LJA - KA

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.973832, 0.225686, -0.026788), (0.227009, 0.971583, -0.067038), (0.010897, -0.071365, -0.997391)14.75431, -7.21084, -158.33777
3given(0.293178, -0.955726, 0.025198), (-0.954243, -0.294143, -0.053846), (0.058874, -0.008259, -0.998231)14.26089, -5.21534, -157.30489
4given(-0.488614, 0.87193, -0.031536), (-0.872323, -0.487467, 0.037802), (0.017588, 0.04598, 0.998788)48.39155, -75.17809, 2.9112
5given(0.68116, 0.731497, -0.030536), (0.731239, -0.681797, -0.021009), (-0.036187, -0.008019, -0.999313)37.77964, -93.49619, -154.88553
6given(-0.504157, -0.86358, 0.007474), (0.860962, -0.501913, 0.082625), (-0.067602, 0.04809, 0.996553)48.53348, -75.88112, 2.59869
7given(0.40282, -0.913019, -0.064283), (-0.914726, -0.399142, -0.062942), (0.031809, 0.084156, -0.995945)-13.15497, -113.33179, -218.84412
8given(-0.584406, 0.810623, 0.036884), (-0.810109, -0.585452, 0.03114), (0.046836, -0.011681, 0.998834)57.04783, -26.49594, 66.78764
9given(-0.992508, 0.119877, 0.023598), (0.119128, 0.992397, -0.030941), (-0.027127, -0.027898, -0.999243)56.02909, -37.91513, -223.07962
10given(-0.39736, -0.916536, -0.04547), (0.915501, -0.399336, 0.048871), (-0.06295, -0.022208, 0.99777)-45.72617, -17.19693, 65.66596
11given(0.994087, 0.104733, 0.028666), (-0.106638, 0.991398, 0.075885), (-0.020472, -0.078493, 0.996704)15.53409, 61.16754, 61.34599
12given(0.601806, 0.797259, 0.046984), (0.798584, -0.601427, -0.023409), (0.009594, 0.051608, -0.998621)91.73759, -121.42766, -218.7462

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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: 37807.586 Da / Num. of mol.: 12
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.: 12 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-GFB / GUANOSINE-5'-DIPHOSPHATE-BETA-L-FUCOPYRANOSE


Mass: 589.342 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C16H25N5O15P2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsMHHHHHHSSGVDLGTENLYFQS AT START DUE TO EXPRESSION TAG

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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: 2.17 Å3/Da / Density % sol: 43.36 % / Description: NONE
Crystal growDetails: 0.1M BIS-TRIS-PROPANE PH 7.5, 0.15M SODIUM CHLORIDE, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9611
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9611 Å / Relative weight: 1
ReflectionResolution: 2.6→29.64 Å / Num. obs: 113998 / % possible obs: 97.4 % / Observed criterion σ(I): 3.3 / Redundancy: 2.1 % / Biso Wilson estimate: 42.5 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 61.2
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 2.1 % / Rmerge(I) obs: 1.15 / Mean I/σ(I) obs: 3.3 / % possible all: 78.1

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Processing

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

4b8w


Resolution: 2.6→29.66 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.864 / SU B: 35.659 / SU ML: 0.342 / Cross valid method: THROUGHOUT / ESU R Free: 0.403 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.28565 5653 5 %RANDOM
Rwork0.22163 ---
obs0.22482 107442 96.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.598 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å20.2 Å2-0.37 Å2
2--0.27 Å2-0.3 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28839 0 1036 41 29916
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01930721
X-RAY DIFFRACTIONr_bond_other_d0.0020.0227004
X-RAY DIFFRACTIONr_angle_refined_deg1.381.96542152
X-RAY DIFFRACTIONr_angle_other_deg0.8163.00661623
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.55353793
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.71124.0941336
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.449154143
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.52415115
X-RAY DIFFRACTIONr_chiral_restr0.0690.24755
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02135146
X-RAY DIFFRACTIONr_gen_planes_other0.0010.027549
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_it1.433.22915208
X-RAY DIFFRACTIONr_mcbond_other1.433.22915207
X-RAY DIFFRACTIONr_mcangle_it2.3384.84418989
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.3243.29515513
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
Refine LS restraints NCS

Ens-ID: 1 / Number: 126 / Refine-ID: X-RAY DIFFRACTION / Type: tight thermal / Weight position: 0.5

Dom-IDAuth asym-IDRms dev position (Å)
1A5.76
2B3.88
3C7.47
4D4.29
5E6.64
6F5.89
7G2.61
8H4.5
9I2.6
10J7.59
11K6.91
12L6.05
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 305 -
Rwork0.334 6080 -
obs--73.73 %
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)
12.3867-0.4270.31421.76070.72951.0747-0.096-0.14320.12850.23690.0512-0.1020.0536-0.06620.04480.0923-0.0030.01930.06690.00250.057119.6742-33.6027-62.4496
21.07690.60520.01321.1134-0.29190.9462-0.11790.11930.1862-0.31880.09260.06760.03380.02960.02530.1004-0.0206-0.00390.04330.0590.0898-10.022-31.5818-94.1631
31.7408-0.13520.60371.2238-0.0330.706-0.19230.3468-0.0045-0.23080.2273-0.06740.00450.1023-0.0350.1011-0.07090.02580.1737-0.01230.031134.68682.2487-93.4346
40.68480.3163-0.10892.7776-0.63240.52960.055-0.17720.11160.4388-0.10730.1723-0.0598-0.01430.05230.0739-0.02150.0370.0934-0.04790.0516-23.3429-48.2987-62.8908
51.191-0.0639-0.22061.58350.07290.73190.22270.4135-0.048-0.1725-0.20790.0402-0.093-0.0407-0.01480.06850.08220.00630.2328-0.01980.056727.9379-54.221-93.3302
61.90220.5352-0.03460.8297-0.06890.96180.0244-0.1106-0.35620.2141-0.0228-0.207-0.0068-0.006-0.00160.07880.025-0.03260.04410.02710.085555.340.5889-61.3409
71.2098-0.45970.31930.614-0.13440.7945-0.02660.3045-0.1178-0.076-0.0169-0.03560.12610.09460.04350.0508-0.03490.04390.1239-0.06390.0501-54.0871-48.8313-163.2626
81.04970.0635-0.33752.3059-0.34051.2185-0.1013-0.34410.10520.25580.06760.1607-0.074-0.14630.03370.04430.06050.00190.1926-0.04180.030921.6871-24.4992-130.7099
91.00030.3424-0.16050.7654-0.31920.4244-0.05260.13190.046-0.3824-0.00990.06030.0712-0.03750.06240.23820.0263-0.06930.04350.01830.079131.7603-4.916-161.9642
102.29330.75840.411.6214-0.12940.79190.0437-0.1801-0.33940.5072-0.0672-0.16740.2026-0.00410.02340.30610.01690.01050.07230.05410.0709-32.973-50.4141-131.7283
112.0201-0.6878-0.67972.4860.8981.6392-0.059-0.19840.03010.5776-0.0482-0.14190.09410.21520.10720.1811-0.0587-0.06010.08230.04710.041616.4264-83.7983-130.3523
121.34360.10780.23642.30920.2490.94880.04450.37370.0045-0.443-0.26880.0149-0.12270.10280.22430.11110.09960.00290.26390.09630.111928.2415-101.6902-161.7899
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 902
2X-RAY DIFFRACTION2B-6 - 902
3X-RAY DIFFRACTION3C-7 - 902
4X-RAY DIFFRACTION4D-1 - 902
5X-RAY DIFFRACTION5E-7 - 902
6X-RAY DIFFRACTION6F8 - 902
7X-RAY DIFFRACTION7G-7 - 902
8X-RAY DIFFRACTION8H-1 - 902
9X-RAY DIFFRACTION9I-7 - 902
10X-RAY DIFFRACTION10J8 - 902
11X-RAY DIFFRACTION11K8 - 902
12X-RAY DIFFRACTION12L-7 - 902

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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

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