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- PDB-5uzh: Crystal structure of a GDP-mannose dehydratase from Naegleria fowleri -

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Basic information

Entry
Database: PDB / ID: 5uzh
TitleCrystal structure of a GDP-mannose dehydratase from Naegleria fowleri
ComponentsNafoA.00085.b
KeywordsTRANSFERASE / SSGCID / Naegleria fowleri / kinase / nucloside diphosphate / potential drug target / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


GDP-mannose 4,6-dehydratase / GDP-mannose 4,6-dehydratase activity / GDP-mannose metabolic process / nucleotide binding
Similarity search - Function
GDP-mannose 4,6-dehydratase / GDP-mannose 4,6 dehydratase / NAD(P)-binding domain / UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / 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-mannose 4,6-dehydratase
Similarity search - Component
Biological speciesNaegleria fowleri (brain-eating amoeba)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsSSGCID / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of a GDP-mannose dehydratase from Naegleria fowleri
Authors: Conrady, D.G. / Lorimer, D. / Edwards, T.E.
History
DepositionFeb 26, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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

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Assembly

Deposited unit
A: NafoA.00085.b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8507
Polymers39,2731
Non-polymers1,5776
Water2,846158
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, SEC determined molecular weight is consistent with monomer.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.730, 92.730, 94.660
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-405-

MPD

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Components

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Protein , 1 types, 1 molecules A

#1: Protein NafoA.00085.b


Mass: 39272.957 Da / Num. of mol.: 1 / Fragment: NafoA.00085.b
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Naegleria fowleri (brain-eating amoeba)
Strain: ATCC 30863 / Plasmid: NafoA.00085.b.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A0A1W2VMZ8*PLUS, GDP-mannose 4,6-dehydratase

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Non-polymers , 5 types, 164 molecules

#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: 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
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.59 Å3/Da / Density % sol: 52.52 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Rigaku Reagents Morpheus F12: (0.02M each D-Glucose, D-Mannnose, D-Galactose, L-Fucose, D-Xylose, N-acetyl-D-Glucosamine: 0.1 M Tris (base)/Bicine pH 8.5, 12.5% MPD, 12.5% Peg1K, 12.5% ...Details: Rigaku Reagents Morpheus F12: (0.02M each D-Glucose, D-Mannnose, D-Galactose, L-Fucose, D-Xylose, N-acetyl-D-Glucosamine: 0.1 M Tris (base)/Bicine pH 8.5, 12.5% MPD, 12.5% Peg1K, 12.5% PEG3350) mixed 1:1 with 19.8 mg/mL protein in sitting drop vapor diffusion. Tray id 283244f12, puck kjy4-9.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 9, 2016 / 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→46.365 Å / Num. obs: 20179 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 9.611 % / Biso Wilson estimate: 33.65 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.075 / Rrim(I) all: 0.079 / Χ2: 1.003 / Net I/σ(I): 24.67
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.25-2.319.8050.5665.1814620.9340.597100
2.31-2.379.8050.5035.814410.9460.53100
2.37-2.449.8350.4187.0413780.9640.4499.9
2.44-2.529.8180.3458.413400.9730.36499.9
2.52-2.69.8280.27110.2413050.9860.286100
2.6-2.699.8130.23311.7212680.9880.245100
2.69-2.799.760.18114.4912310.9920.191100
2.79-2.99.7670.14817.3811850.9940.156100
2.9-3.039.7560.11621.1211320.9960.123100
3.03-3.189.7330.09125.2110920.9980.096100
3.18-3.359.6860.0730.8610430.9990.07499.9
3.35-3.569.590.05637.139920.9990.05999.8
3.56-3.89.540.04741.939240.9990.05100
3.8-4.119.3460.0447.758740.9990.04299.9
4.11-4.59.3370.03552.658150.9990.037100
4.5-5.039.2870.03255.277390.9990.03499.9
5.03-5.819.1920.03354.1766110.03599.8
5.81-7.129.0530.03354.295700.9990.035100
7.12-10.068.6570.0360.554550.9990.032100
10.06-46.3657.3350.03255.952720.9990.03497.1

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXdev_2621refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T2A

1t2a


Resolution: 2.25→46.365 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.45
RfactorNum. reflection% reflection
Rfree0.199 2004 9.93 %
Rwork0.1468 --
obs0.1521 20178 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 98.57 Å2 / Biso mean: 36.8162 Å2 / Biso min: 16.99 Å2
Refinement stepCycle: final / Resolution: 2.25→46.365 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2712 0 101 159 2972
Biso mean--36.04 40.75 -
Num. residues----345
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072883
X-RAY DIFFRACTIONf_angle_d0.883926
X-RAY DIFFRACTIONf_chiral_restr0.052436
X-RAY DIFFRACTIONf_plane_restr0.006506
X-RAY DIFFRACTIONf_dihedral_angle_d8.8262322
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.2501-2.30630.24191500.170112701420
2.3063-2.36870.26331260.163712791405
2.3687-2.43840.23611140.164212911405
2.4384-2.51710.23821450.152412611406
2.5171-2.6070.22571650.149212521417
2.607-2.71140.23541270.154512961423
2.7114-2.83480.19241390.152212871426
2.8348-2.98420.19591340.152112951429
2.9842-3.17120.22531370.153413001437
3.1712-3.41590.18951320.144713001432
3.4159-3.75960.17071760.134712751451
3.7596-4.30320.16991280.121213351463
4.3032-5.42030.15931570.131413251482
5.4203-46.37480.23041740.172714081582
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)
14.478-0.3320.11772.6601-0.23842.76470.12580.2466-0.586-0.32610.02650.10870.39190.026-0.15870.33180.0279-0.05870.2346-0.04140.2503-18.8423-12.16-13.7929
21.2794-0.0223-0.10531.1773-0.41870.81070.00090.1051-0.0264-0.01590.05350.10090.031-0.0933-0.0560.21550.0242-0.00760.23930.03220.2047-21.87652.712-4.3559
33.13442.4272-1.51612.8123-1.29532.6940.3491-0.347-0.03790.4573-0.16920.3274-0.1492-0.2582-0.18260.27350.0390.06350.34510.05540.3033-36.5731-2.610414.9902
44.50072.4821-1.55047.9599-6.6197.12650.00460.1609-0.0867-0.22390.40660.66140.2575-0.6353-0.50470.2296-0.0257-0.04680.34680.01820.2464-38.0211-4.6727-4.8478
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 33 through 98 )A33 - 98
2X-RAY DIFFRACTION2chain 'A' and (resid 99 through 289 )A99 - 289
3X-RAY DIFFRACTION3chain 'A' and (resid 290 through 345 )A290 - 345
4X-RAY DIFFRACTION4chain 'A' and (resid 346 through 377 )A346 - 377

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