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- PDB-7kn1: Crystal structure of UDP-glucose-4-epimerase (galE) from Stenotro... -

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Basic information

Entry
Database: PDB / ID: 7kn1
TitleCrystal structure of UDP-glucose-4-epimerase (galE) from Stenotrophomonas maltophila with bound NAD and formylated UDP-arabinopyranose
ComponentsUDP-glucose 4-epimerase
KeywordsISOMERASE / SSGCID / UDP-glucose-4-epimerase / UDP-xylose-4-epimerase / galE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


UDP-glucose 4-epimerase / UDP-glucose 4-epimerase activity / galactose metabolic process / nucleotide binding
Similarity search - Function
UDP-glucose 4-epimerase / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / UDP-4-deoxy-4-formamido-beta-L-arabinopyranose / UDP-glucose 4-epimerase
Similarity search - Component
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal structure of UDP-glucose-4-epimerase (galE) from Stenotrophomonas maltophila with bound NAD and formylated UDP-arabinopyranose
Authors: Bolejack, M.J. / Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionNov 3, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 21, 2021Group: Other / Structure summary
Category: audit_author / pdbx_SG_project ...audit_author / pdbx_SG_project / pdbx_database_status / struct_keywords
Item: _pdbx_database_status.SG_entry / _struct_keywords.text
Revision 1.2Oct 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: UDP-glucose 4-epimerase
B: UDP-glucose 4-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,11421
Polymers76,7292
Non-polymers3,38419
Water15,601866
1
A: UDP-glucose 4-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,08811
Polymers38,3651
Non-polymers1,72310
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UDP-glucose 4-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,02610
Polymers38,3651
Non-polymers1,6619
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.270, 79.420, 153.850
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein UDP-glucose 4-epimerase


Mass: 38364.543 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stenotrophomonas maltophilia (strain K279a) (bacteria)
Strain: K279a / Gene: galE, Smlt3413 / Plasmid: StmaA.00085.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B2FNY6, UDP-glucose 4-epimerase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-WQD / UDP-4-deoxy-4-formamido-beta-L-arabinopyranose / [[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{R},4~{S},5~{S})-5-formamido-3,4-bis(oxidanyl)oxan-2-yl] hydrogen phosphate


Mass: 563.301 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N3O16P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 866 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.88 Å3/Da / Density % sol: 57.25 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5
Details: StmaA.00085.a.B1.PW38702 at 24.25 mg/ml was combined 1:1 (0.4 uL protein/precipitant) with 0.2 M Ammonium citrate dibasic, pH 5.0, and 20% (w/v) PEG 3350 and stored at 14C. No additional ...Details: StmaA.00085.a.B1.PW38702 at 24.25 mg/ml was combined 1:1 (0.4 uL protein/precipitant) with 0.2 M Ammonium citrate dibasic, pH 5.0, and 20% (w/v) PEG 3350 and stored at 14C. No additional ligand was added for crystallization. Tray 312986f3; puck ocs5-3.

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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-300 / Detector: CCD / Date: Nov 21, 2019
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.45→43.08 Å / Num. obs: 156730 / % possible obs: 99.8 % / Redundancy: 5.851 % / Biso Wilson estimate: 18.147 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.079 / Rrim(I) all: 0.087 / Χ2: 0.972 / Net I/σ(I): 13.43 / Num. measured all: 917081 / Scaling rejects: 28
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
1.45-1.496.030.4853.926913511467114650.8930.53100
1.49-1.536.0250.4044.766765411234112290.920.442100
1.53-1.576.0170.3345.736572610927109230.9440.365100
1.57-1.625.9840.2726.886344410610106030.9570.29999.9
1.62-1.675.9840.2357.836138210263102580.9680.258100
1.67-1.735.9360.1969.0959057996199490.9770.21599.9
1.73-1.85.9050.16210.5256515957895700.9830.17899.9
1.8-1.875.8430.13612.0854150927592680.9870.1599.9
1.87-1.965.7650.11313.8851357892489090.9890.12599.8
1.96-2.055.7090.09515.6948385849284750.9920.10499.8
2.05-2.165.660.08217.6545651808780650.9920.0999.7
2.16-2.295.660.07518.8643456770276780.9930.08299.7
2.29-2.455.6730.0719.9440850722072010.9940.07799.7
2.45-2.655.7090.06521.3138442676767340.9950.07199.5
2.65-2.95.7180.05922.8135555624262180.9950.06599.6
2.9-3.245.7070.05523.8732068564356190.9960.06199.6
3.24-3.745.7530.04925.4528800502750060.9960.05499.6
3.74-4.595.7850.04626.4624702428042700.9970.05199.8
4.59-6.485.9060.04326.5619826336833570.9970.04799.7
6.48-43.085.6520.03626.4210926195519330.9980.0498.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.19rc-4022refinement
PDB_EXTRACT3.27data extraction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1udc

1udc


Resolution: 1.45→43.08 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1768 2014 1.29 %
Rwork0.1593 154619 -
obs0.1596 156633 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.2 Å2 / Biso mean: 16.1919 Å2 / Biso min: 4.73 Å2
Refinement stepCycle: final / Resolution: 1.45→43.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5090 0 220 888 6198
Biso mean--15.68 30.41 -
Num. residues----672
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
1.45-1.490.24531390.21231088411023
1.49-1.530.20771310.19271099211123
1.53-1.570.21651390.18531098511124
1.57-1.620.19581440.18091094711091
1.62-1.680.19591490.17651097111120
1.68-1.750.20191310.1751093611067
1.75-1.830.19041500.1691098811138
1.83-1.920.16651470.16591102711174
1.92-2.040.19881450.16321099211137
2.04-2.20.16571300.1591105611186
2.2-2.420.17741490.16081104811197
2.42-2.770.1771660.15751106411230
2.77-3.490.16221500.14511117211322
3.49-43.080.1491440.13591155711701
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)
10.493-0.08430.27280.755-0.12181.4399-0.01740.03270.0825-0.0007-0.01560.0107-0.1151-0.0030.03520.0534-0.0057-0.00270.05680.00030.0666-8.5539-11.17037.4718
21.58520.0450.37080.6621-0.23921.21660.0554-0.0848-0.17170.0365-0.00330.02730.1642-0.1161-0.02590.0716-0.0122-0.00350.08530.01560.0693-16.7927-27.549313.6158
30.5514-0.0255-0.10070.63840.33541.10510.0210.01840.01220.01010.012-0.0130.064-0.0246-0.04270.060.0034-0.02040.08330.00340.073-16.7279-24.5254-1.2857
40.6013-0.206-0.33030.78980.35611.67860.04890.0957-0.0347-0.0533-0.0015-0.03080.059-0.0102-0.03640.06630.0032-0.03060.1185-0.00410.0771-17.0113-27.6002-9.5746
50.9890.01940.10790.5471-0.14631.4283-0.0133-0.01910.00620.05150.0003-0.0692-0.0470.08730.01580.0726-0.0054-0.00160.04410.00280.06566.3702-23.426535.0623
60.3247-0.06870.45051.5483-0.31260.89780.01270.0471-0.1077-0.09720.05780.19670.1135-0.1031-0.03210.0778-0.0132-0.00980.05710.00690.0766-6.9202-35.674128.3604
70.70160.0976-0.42360.77660.04451.42130.01190.0118-0.00260.05910.01120.0425-0.0671-0.1329-0.01280.08410.02290.00430.05880.02440.0729-6.4922-36.231744.9295
82.6387-0.3641-0.21684.157-0.83951.83660.1707-0.2210.23620.3346-0.0868-0.0228-0.39040.0047-0.05350.19940.01260.03540.10230.00110.0779-1.5696-29.27257.8008
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 114 )A-1 - 114
2X-RAY DIFFRACTION2chain 'A' and (resid 115 through 165 )A115 - 165
3X-RAY DIFFRACTION3chain 'A' and (resid 166 through 267 )A166 - 267
4X-RAY DIFFRACTION4chain 'A' and (resid 268 through 334 )A268 - 334
5X-RAY DIFFRACTION5chain 'B' and (resid 0 through 114 )B0 - 114
6X-RAY DIFFRACTION6chain 'B' and (resid 115 through 165 )B115 - 165
7X-RAY DIFFRACTION7chain 'B' and (resid 166 through 316 )B166 - 316
8X-RAY DIFFRACTION8chain 'B' and (resid 317 through 335 )B317 - 335

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