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- PDB-7ll6: Crystal structure of fucose synthetase family protein from Brucel... -

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Basic information

Entry
Database: PDB / ID: 7ll6
TitleCrystal structure of fucose synthetase family protein from Brucella suis ATCC 23445
ComponentsGDP-L-fucose synthase
KeywordsOXIDOREDUCTASE / SSGCID / GDP-L-fucose synthase / NADP / GDP-4-dehydro-6-deoxy-D-mannose / GDP-fucose / 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 suis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be published
Title: Crystal structure of fucose synthetase family protein from Brucella suis ATCC 23445
Authors: Abendroth, J. / Horanyi, P.S. / Lorimer, D.D. / Edwards, T.E.
History
DepositionFeb 3, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)37,6853
Polymers36,9171
Non-polymers7682
Water1,08160
1
A: GDP-L-fucose synthase
hetero molecules

A: GDP-L-fucose synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,3696
Polymers73,8342
Non-polymers1,5354
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area5480 Å2
ΔGint-42 kcal/mol
Surface area22860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.650, 75.650, 112.340
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-535-

HOH

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Components

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


Mass: 36916.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella suis (strain ATCC 23445 / NCTC 10510) (bacteria)
Strain: ATCC 23445 / NCTC 10510 / Gene: fcl, BSUIS_B0421 / Plasmid: Brsub.00085.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A9WYA5, 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.52 Å3/Da / Density % sol: 51.2 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: Microlytic MCSG1 screen: 3.5M sodium formate, 100mM sodium acetate / HCl pH 4.6: BrsuB.00085.a.B1.PS02124 at 20mg/ml + NADP: tray 257990 h6: cryo: direct: puck xbm5-2.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 12, 2014 / Details: Beryllium Lenses
RadiationMonochromator: Diamond (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 18199 / % possible obs: 99.8 % / Redundancy: 8.182 % / Biso Wilson estimate: 56.85 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.069 / Rrim(I) all: 0.074 / Χ2: 0.92 / Net I/σ(I): 17.32
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.25-2.318.3390.6283.4213130.90.67100
2.31-2.378.3110.4594.5613100.940.49100
2.37-2.448.3060.3685.5812530.9680.393100
2.44-2.528.3250.2926.8512160.9790.311100
2.52-2.68.3360.2238.3911860.9870.238100
2.6-2.698.2960.1989.5911360.990.211100
2.69-2.798.3230.15711.7611160.9920.167100
2.79-2.918.2810.11315.1810730.9960.12100
2.91-3.038.2730.08718.4610230.9980.093100
3.03-3.188.2570.08419.849770.9970.089100
3.18-3.358.2390.06624.589420.9970.071100
3.35-3.568.2140.06127.318970.9980.06599.9
3.56-3.88.1630.05829.118360.9980.06299.9
3.8-4.118.0680.05531.547920.9980.05999.9
4.11-4.58.0510.05533.17300.9970.05999.9
4.5-5.037.9490.05633.536610.9970.06100
5.03-5.817.890.05332.825890.9970.057100
5.81-7.127.7830.05333.65080.9970.05799.4
7.12-10.067.3580.05434.074080.9970.05999.5
10.06-506.2450.05231.472330.9960.05792.1

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Processing

Software
NameVersionClassification
PHENIX1.194092refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1e6u chain A as per MoRDa

1e6u


Resolution: 2.25→42.64 Å / SU ML: 0.249 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.2189
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2329 1764 9.71 %0
Rwork0.2071 16401 --
obs0.2099 18165 99.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 74.82 Å2
Refinement stepCycle: LAST / Resolution: 2.25→42.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2084 0 49 60 2193
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00632190
X-RAY DIFFRACTIONf_angle_d0.85093001
X-RAY DIFFRACTIONf_chiral_restr0.0501351
X-RAY DIFFRACTIONf_plane_restr0.007405
X-RAY DIFFRACTIONf_dihedral_angle_d12.9342771
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.310.25991330.23361231X-RAY DIFFRACTION100
2.31-2.380.26921350.21391250X-RAY DIFFRACTION100
2.38-2.460.2681210.22821252X-RAY DIFFRACTION100
2.46-2.540.22191460.21071242X-RAY DIFFRACTION100
2.54-2.650.28131060.2361245X-RAY DIFFRACTION100
2.65-2.770.27381270.25421275X-RAY DIFFRACTION100
2.77-2.910.23481200.24341271X-RAY DIFFRACTION100
2.91-3.090.2591660.2311208X-RAY DIFFRACTION99.93
3.09-3.330.29051060.23571297X-RAY DIFFRACTION100
3.33-3.670.23491380.22321256X-RAY DIFFRACTION99.86
3.67-4.20.18961270.17921299X-RAY DIFFRACTION99.86
4.2-5.280.20541810.18151235X-RAY DIFFRACTION99.93
5.29-42.640.24011580.19261340X-RAY DIFFRACTION98.62
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)
12.27129282613-0.000260708296927-0.596427049412.85334149936-0.4357970117563.213597208870.363198766393-0.609296289734-0.1405530694281.39323246579-0.864767981265-0.9763750412670.1361572784531.242128777210.3261334401510.863458785404-0.254630109442-0.3405124495470.8341837255680.2835535515420.694198711863-22.0635291401-4.70310720587-2.22479862728
22.807594793380.866012399430.756638878944.44913304485-1.041407323674.598905994070.318642002231-0.3396107320190.1011003010290.55283762024-0.5313811042810.159702326762-0.07878397869990.292819963330.2038023212310.42472831538-0.155333007220.005522332748930.2826761158550.04423450015980.353248654782-34.9105329624-1.86147944457-10.9317907374
32.023793570440.3739582814510.4981429665142.10226211581-0.6701477396114.68673878520.298020924183-0.280040419143-0.1124648761070.963065766708-0.602667559375-0.02763998515660.5215085017660.3469431334050.2823637973570.56952444636-0.141896497237-0.006580979320850.3365976875440.1055024159830.396091671196-33.4627725786-5.73405035092-9.16960614349
42.480910640491.399543568131.201725789834.952744984121.434088466710.7063719452630.627230942966-0.8689381219350.4676074248331.49850345082-1.19256262341.35009414420.471576714434-0.6927426237790.04322562034171.42830742854-0.5445338130890.3599599237830.724135929561-0.073794539690.580078498363-37.23145529664.521607733149.14043749513
55.408886933541.020793517050.2054060733842.313048061292.465789287673.36169416906-0.00623358325023-0.2004086507-0.06615878410150.996327225882-0.5672632134981.427628535180.478547467111-0.1201487407360.5674316032480.947352115737-0.3093370581190.1737325906690.462723465574-0.02863614669860.494258784615-40.232371585-11.4172015154-3.37066634274
61.15324532072-0.838778860831-1.813123928942.406407784212.299800134495.184646807-0.13233844102-0.181068722221-0.3758250685290.82546597599-0.5986794517710.9320284920070.485641059699-0.6046612211990.06906188298361.94609756281-0.6938079860641.020947876571.2587178462-0.6415622323211.61236761025-47.62875934368.6806385268915.3283750277
72.03342500462-0.59944847901-0.2240943845581.09500197611.331451502071.749256381560.38821389282-0.7471217992820.08805557328311.72740203587-0.4331059123310.7152794499140.103437507803-0.2588977230830.03956158635741.29604311618-0.4435866054250.3035083483410.788950541083-0.04279649264780.717853239023-44.6171164326-6.168302357546.28204965591
80.935050631482-0.02691321774780.5994676057260.8456252301220.2641515148740.602251784612-0.37396102897-0.7324607303930.3994443544120.801575049990.186376673496-0.0509511434114-0.4166395947650.678207470913-0.243557422812.34632576119-0.6615893648090.1965420377111.49400376547-0.4179864083030.503849091443-35.61504582766.6282500808118.7084507159
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 12 through 89 )12 - 891 - 78
22chain 'A' and (resid 90 through 147 )90 - 14779 - 136
33chain 'A' and (resid 148 through 185 )148 - 185137 - 174
44chain 'A' and (resid 186 through 241 )186 - 241175 - 221
55chain 'A' and (resid 242 through 254 )242 - 254222 - 234
66chain 'A' and (resid 255 through 269 )255 - 269235 - 249
77chain 'A' and (resid 270 through 305 )270 - 305250 - 271
88chain 'A' and (resid 306 through 320 )306 - 320272 - 286

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