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- PDB-8du1: Crystal Structure of NAD bound dTDP-glucose 4,6-dehydratase from ... -

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Basic information

Entry
Database: PDB / ID: 8du1
TitleCrystal Structure of NAD bound dTDP-glucose 4,6-dehydratase from Elizabethkingia anophelis
ComponentsdTDP-glucose 4,6-dehydratase
KeywordsLYASE / SSGCID / nucleotide-sugar metabolic process / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homologydTDP-glucose 4,6-dehydratase / dTDP-glucose 4,6-dehydratase / dTDP-glucose 4,6-dehydratase activity / nucleotide-sugar metabolic process / GDP-mannose 4,6 dehydratase / NAD(P)-binding domain / NAD(P)-binding domain superfamily / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / dTDP-glucose 4,6-dehydratase
Function and homology information
Biological speciesElizabethkingia anophelis NUHP1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: to be published
Title: Crystal Structure of DNA Polymerase III beta subunit from Elizabethkingia anophelis
Authors: DeBouver, N.D. / Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionJul 26, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: dTDP-glucose 4,6-dehydratase
B: dTDP-glucose 4,6-dehydratase
C: dTDP-glucose 4,6-dehydratase
D: dTDP-glucose 4,6-dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,60926
Polymers168,0204
Non-polymers3,58922
Water23,9061327
1
A: dTDP-glucose 4,6-dehydratase
C: dTDP-glucose 4,6-dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,80413
Polymers84,0102
Non-polymers1,79411
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6660 Å2
ΔGint-40 kcal/mol
Surface area28690 Å2
MethodPISA
2
B: dTDP-glucose 4,6-dehydratase
D: dTDP-glucose 4,6-dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,80413
Polymers84,0102
Non-polymers1,79411
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6720 Å2
ΔGint-38 kcal/mol
Surface area29100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.740, 84.620, 130.870
Angle α, β, γ (deg.)90.000, 101.180, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
dTDP-glucose 4,6-dehydratase


Mass: 42004.910 Da / Num. of mol.: 4 / Fragment: ElanA.00085.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Elizabethkingia anophelis NUHP1 (bacteria)
Gene: BD94_3274 / Plasmid: ElanA.00085.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A077ELH2, dTDP-glucose 4,6-dehydratase

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Non-polymers , 5 types, 1349 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1327 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.16 Å3/Da / Density % sol: 42.99 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7
Details: [Target: ElanA.00085.a.B1.PS38380 - 21.5 mg/mL] [Barcode: 324703c1] [Pin: iyi1-8] [Crystallization: sparse screen - MCSG4 C1 - 0.1 M Bis-Tris Propane:HCl pH 7, 2 M Di-Ammonium Hydrogen ...Details: [Target: ElanA.00085.a.B1.PS38380 - 21.5 mg/mL] [Barcode: 324703c1] [Pin: iyi1-8] [Crystallization: sparse screen - MCSG4 C1 - 0.1 M Bis-Tris Propane:HCl pH 7, 2 M Di-Ammonium Hydrogen Citrate, 14C, 0.2:0.2 drop ratio] [Cryo: 20% EG]

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 14, 2022 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.85→42.8 Å / Num. obs: 121703 / % possible obs: 99.8 % / Redundancy: 5.411 % / Biso Wilson estimate: 23.7 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rrim(I) all: 0.071 / Χ2: 0.929 / Net I/σ(I): 16.26 / Num. measured all: 658558 / Scaling rejects: 54
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.85-1.94.6610.5132.5941533898289110.8370.5899.2
1.9-1.955.3850.4373.4347160875587580.90.484100
1.95-2.015.4910.324.846629850084920.9450.35399.9
2.01-2.075.4940.2496.0745473828182770.9670.276100
2.07-2.145.5090.2077.3744188802380210.9770.229100
2.14-2.215.5070.1768.6442561773577290.9820.19599.9
2.21-2.295.5230.14510.4641621754675360.9880.1699.9
2.29-2.395.5150.12312.2239556717871730.9910.13699.9
2.39-2.495.5110.10514.2338030689969010.9930.116100
2.49-2.625.5190.0916.3836355658865870.9950.099100
2.62-2.765.5180.07619.4434868632163190.9960.083100
2.76-2.935.5020.06522.4632803597459620.9970.07299.8
2.93-3.135.4850.05426.3130660559355900.9980.05999.9
3.13-3.385.4530.04630.528487524152240.9980.05199.7
3.38-3.75.430.0434.6626075481048020.9980.04499.8
3.7-4.145.4290.03638.4823540434943360.9990.03999.7
4.14-4.785.390.03440.0420847387438680.9990.03899.8
4.78-5.855.3940.03339.3817605326732640.9990.03799.9
5.85-8.275.3280.0343913607255325540.9990.037100
8.27-42.84.9750.03440.626960143713990.9990.03897.4

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.20-4487refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold2

Resolution: 1.85→42.8 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1948 2071 1.7 %
Rwork0.1555 119601 -
obs0.1562 121672 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.04 Å2 / Biso mean: 31.5382 Å2 / Biso min: 10.39 Å2
Refinement stepCycle: final / Resolution: 1.85→42.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11386 0 230 1355 12971
Biso mean--22.67 36.07 -
Num. residues----1432
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.890.2831260.22897870799699
1.89-1.940.22811480.19779288076100
1.94-1.990.21181450.171479458090100
1.99-2.050.21861380.160879518089100
2.05-2.120.22051200.161979728092100
2.12-2.190.22151250.160779458070100
2.19-2.280.22621170.162879998116100
2.28-2.390.19091330.160879858118100
2.39-2.510.22841550.161379458100100
2.51-2.670.21761160.160579948110100
2.67-2.870.21361640.165579508114100
2.87-3.160.21251090.162280398148100
3.16-3.620.17581480.143279758123100
3.62-4.560.14851880.127479678155100
4.56-42.80.19451390.15538136827599
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)
15.1297-0.12181.44292.6775-1.43383.1750.0763-0.3338-0.1690.27580.0443-0.07750.22110.2049-0.08160.18730.0194-0.0570.1734-0.04180.11588.25770.041320.2083
21.3571-0.4012-0.44621.460.11331.48320.0385-0.23430.13110.08550.041-0.27130.01850.1983-0.05410.1323-0.0171-0.06140.1736-0.04160.185215.01434.531912.3029
31.0179-0.3614-0.77910.98550.26011.26250.00810.0665-0.0438-0.0741-0.02580.00510.1041-0.10250.0040.1085-0.0086-0.03010.1248-0.01150.11745.6367-4.20752.0702
41.1487-0.2756-1.17381.39130.53550.83740.02270.3537-0.121-0.0527-0.14010.19830.0818-0.16020.02510.1512-0.0319-0.04470.1931-0.02180.1291-6.6243-4.30278.038
52.8107-1.3695-0.70821.3550.38470.81220.05660.4645-0.077-0.12-0.17970.16570.0423-0.33530.07710.1724-0.0383-0.04310.2799-0.03870.2084-15.532-5.40656.411
63.23620.9314-1.12644.3708-0.41161.79480.1845-0.27780.43320.3438-0.02230.0522-0.2408-0.013-0.0770.150.0138-0.00230.2057-0.02820.1418-7.242410.844418.7279
71.2998-0.0674-0.08031.719-0.37751.0720.0492-0.3590.14760.4505-0.0174-0.0429-0.19570.1355-0.07310.2638-0.0097-0.0250.2134-0.0040.1543-36.51666.106483.6811
81.3246-0.1896-0.25081.9867-0.44141.75110.0345-0.2110.00980.0808-0.0709-0.2444-0.06850.2616-0.01850.1176-0.0138-0.02910.15580.02780.1507-27.3133.272870.9819
90.91250.1395-0.9981.0588-0.36081.3462-0.0724-0.0171-0.0763-0.04960.02860.03790.0736-0.1103-0.04640.12240.0001-0.02020.11360.01340.1628-40.0822-4.504366.3175
102.6257-0.2281-0.80640.7206-0.16481.13420.03650.1739-0.1345-0.02440.02310.17750.0273-0.28250.05310.1520.0031-0.01260.18810.05940.1907-56.0614-5.577374.2738
112.7833-0.3811-0.47423.1541-1.34241.62090.2674-0.48810.83680.90360.0590.0993-0.59980.07820.24380.53570.02820.1590.2151-0.02950.4201-49.022616.626983.5118
122.0708-0.2607-1.53281.79680.82583.75290.51170.26570.3956-0.6005-0.1494-0.1524-1.0095-0.33650.08560.52140.13870.12540.13680.06190.181216.07476.2768-19.4934
132.9754-0.3238-0.75321.27530.52732.83750.1639-0.12170.0041-0.07170.0648-0.325-0.1490.4757-0.0120.28580.01640.00610.2892-0.04770.229231.499-7.9975-22.8295
141.88260.3859-0.82582.1723-0.72853.13390.02880.12120.0762-0.0857-0.116-0.0098-0.09590.04060.08980.1550.0221-0.02110.13630.01290.1252-28.417310.880837.4709
151.00250.4859-0.9230.9505-0.78022.5422-0.04760.155-0.1457-0.2328-0.03520.0020.2851-0.12020.02120.1775-0.0027-0.01470.1117-0.01710.1326-35.0694-0.619547.6166
161.92680.18-0.44671.227-0.4751.8856-0.1296-0.0416-0.389-0.1222-0.1966-0.31920.53460.4870.18850.43560.1280.08110.340.05380.276-15.3969-7.832738.7174
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 24 )A-1 - 24
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 135 )A25 - 135
3X-RAY DIFFRACTION3chain 'A' and (resid 136 through 206 )A136 - 206
4X-RAY DIFFRACTION4chain 'A' and (resid 207 through 265 )A207 - 265
5X-RAY DIFFRACTION5chain 'A' and (resid 266 through 323 )A266 - 323
6X-RAY DIFFRACTION6chain 'A' and (resid 324 through 359 )A324 - 359
7X-RAY DIFFRACTION7chain 'B' and (resid 0 through 63 )B0 - 63
8X-RAY DIFFRACTION8chain 'B' and (resid 64 through 135 )B64 - 135
9X-RAY DIFFRACTION9chain 'B' and (resid 136 through 206 )B136 - 206
10X-RAY DIFFRACTION10chain 'B' and (resid 207 through 336 )B207 - 336
11X-RAY DIFFRACTION11chain 'B' and (resid 337 through 358 )B337 - 358
12X-RAY DIFFRACTION12chain 'C' and (resid 0 through 185 )C0 - 185
13X-RAY DIFFRACTION13chain 'C' and (resid 186 through 357 )C186 - 357
14X-RAY DIFFRACTION14chain 'D' and (resid -3 through 96 )D-3 - 96
15X-RAY DIFFRACTION15chain 'D' and (resid 97 through 206 )D97 - 206
16X-RAY DIFFRACTION16chain 'D' and (resid 207 through 359 )D207 - 359

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