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- PDB-7ern: Crystal structure of D-allulose 3-epimerase with D-fructose from ... -

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Basic information

Entry
Database: PDB / ID: 7ern
TitleCrystal structure of D-allulose 3-epimerase with D-fructose from Agrobacterium sp. SUL3
ComponentsD-tagatose 3-epimerase
KeywordsISOMERASE / D-allulose / rare sugar / Agrobacterium sp. SUL3 / D-allulose 3-epimerase
Function / homologyXylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily / D-fructose / D-tagatose 3-epimerase
Function and homology information
Biological speciesAgrobacterium sp. SUL3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsZhu, Z.L. / Miyakawa, T. / Tanokura, M. / Lu, F.P. / Qin, H.-M.
CitationJournal: Adv Sci / Year: 2024
Title: Growth-Coupled Evolutionary Pressure Improving Epimerases for D-Allulose Biosynthesis Using a Biosensor-Assisted In Vivo Selection Platform
Authors: Li, C. / Gao, H. / Li, H. / Wang, T. / Lu, F.P. / Qin, H.-M.
History
DepositionMay 6, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 11, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Feb 7, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D-tagatose 3-epimerase
B: D-tagatose 3-epimerase
C: D-tagatose 3-epimerase
D: D-tagatose 3-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,15912
Polymers122,3424
Non-polymers8188
Water6,287349
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12380 Å2
ΔGint-55 kcal/mol
Surface area36910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.191, 97.953, 160.172
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
D-tagatose 3-epimerase


Mass: 30585.398 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium sp. SUL3 (bacteria) / Gene: AKG12_23230 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta
References: UniProt: A0A0L6K0Q2, Isomerases; Racemases and epimerases; Acting on carbohydrates and derivatives
#2: Sugar
ChemComp-FUD / D-fructose


Type: D-saccharide / Mass: 180.156 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / 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: 2.15 Å3/Da / Density % sol: 42.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M Magnesium chloride, 0.1M Tris pH=8.5, 30% PEG 4000

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Oct 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→46.88 Å / Num. obs: 66104 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 33.81 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.037 / Rrim(I) all: 0.097 / Net I/σ(I): 14.1
Reflection shellResolution: 2.05→2.1 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4343 / CC1/2: 0.75 / Rpim(I) all: 0.43

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7DZ2
Resolution: 2.05→46.84 Å / SU ML: 0.2087 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.8156
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2097 3340 5.06 %
Rwork0.1601 62675 -
obs0.1626 66015 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.11 Å2
Refinement stepCycle: LAST / Resolution: 2.05→46.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8592 0 40 349 8981
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00698820
X-RAY DIFFRACTIONf_angle_d0.813911971
X-RAY DIFFRACTIONf_chiral_restr0.04861313
X-RAY DIFFRACTIONf_plane_restr0.00471574
X-RAY DIFFRACTIONf_dihedral_angle_d9.41881221
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.080.32371430.25392576X-RAY DIFFRACTION99.13
2.08-2.110.31360.242576X-RAY DIFFRACTION99.96
2.11-2.140.25331100.22392602X-RAY DIFFRACTION99.34
2.14-2.180.28981390.21172544X-RAY DIFFRACTION99.85
2.18-2.220.25131630.20392551X-RAY DIFFRACTION99.49
2.22-2.260.25321340.18962587X-RAY DIFFRACTION100
2.26-2.30.32131350.18732566X-RAY DIFFRACTION99.56
2.3-2.350.24431360.18532596X-RAY DIFFRACTION99.93
2.35-2.40.23441300.18882585X-RAY DIFFRACTION99.78
2.4-2.450.25371320.18532624X-RAY DIFFRACTION99.82
2.45-2.510.22551390.1832588X-RAY DIFFRACTION99.89
2.51-2.580.29291340.18722585X-RAY DIFFRACTION99.89
2.58-2.660.22451310.18622611X-RAY DIFFRACTION100
2.66-2.740.23721330.1982606X-RAY DIFFRACTION99.96
2.74-2.840.25931200.18792624X-RAY DIFFRACTION99.96
2.84-2.960.26241550.18812573X-RAY DIFFRACTION99.82
2.96-3.090.25251370.17712607X-RAY DIFFRACTION99.82
3.09-3.250.24241470.18142620X-RAY DIFFRACTION99.89
3.25-3.460.21741370.16752629X-RAY DIFFRACTION99.96
3.46-3.720.18621570.13882609X-RAY DIFFRACTION99.86
3.72-4.10.17211460.11952653X-RAY DIFFRACTION99.86
4.1-4.690.13491400.10792666X-RAY DIFFRACTION99.86
4.69-5.910.15911490.13182683X-RAY DIFFRACTION99.86
5.91-46.840.16921570.14072814X-RAY DIFFRACTION99.8
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.158112938165-0.0895079206006-0.06830872946690.525665867038-0.5597672133980.5488437517560.01107315691350.1076994141640.05742990760040.106355482561-0.08127851531770.0775989683004-0.121570326593-0.1073577722735.34877557475E-50.3118944388020.0131073258433-0.0124655903450.2295677918220.01410707776120.292610312603-27.435047697522.9633645727-12.273274945
20.569505065413-0.1494346466340.01140435604560.296940042024-0.1870775860880.970709321960.01544291190920.119455706433-0.0182652775647-0.0534947504484-0.08278151308260.003449016254850.07237317732680.0748474100622-2.38956383503E-50.2614243786450.02510248202850.02431051964110.246099280212-0.01267615819890.2357226225-21.63724662344.18994589318-9.6648802566
30.0473172215633-0.006054309042250.02623412594080.0401473064976-0.0326020404711-0.00222290065873-0.1206091985170.2057859097320.321052507462-0.1451956492150.1249097944030.2592639568730.0235183250052-0.258721540743-0.0004767735259440.405276623070.00440799497324-0.0306256595940.395925029331-0.0009982409917330.395605275541-40.820107063311.1944821957-4.79499019198
40.10230726682-0.00264692424243-0.1374415767590.0489203805721-0.1507555251210.261719175131-0.226094542103-0.07261782316610.3673314264220.148086841578-0.0530416220776-0.111635093-0.4550464572270.1071420749360.0003393684436540.322201305719-0.00294395244984-0.03470484431910.2090247536460.006637321655770.278912896345-24.062485779919.29579378497.27044922717
50.5683205235710.2451849759470.009432092281870.346439591934-0.08304352177170.04245692579410.0490573601967-0.323969746173-0.8526329506620.230961049773-0.296477566061-0.2505359971170.1280852799440.164327172409-0.01564355164970.3340950392060.03148889858070.001113770498870.3971468752690.1564711573860.554786062847-1.51884052857-13.964911785232.7246427414
60.4448144322390.380292146786-0.3007244272510.641008080641-0.2841744077440.2046455373680.0734329522208-0.290109599457-0.09349777787050.117649227128-0.195779006037-0.146515620274-0.0968484985630.281502158664-4.28238099692E-50.227357194419-0.0303696991862-0.03975481056060.4080844392280.07568179636480.3218529938592.820183651066.362804429633.4152470597
70.08019684274320.04817410875480.1144508464650.200526848609-0.06213086497550.1300101246210.127683721414-0.1850507262350.09662154845560.0188579635585-0.1641329616320.0884644887882-0.05983908798440.0488321575652-0.0001698392878980.217547006355-0.000670110809594-0.004992877334060.2850116245610.03703390652260.25691405658-3.180245099478.6506331117123.9572313111
80.3501632186850.03595761994250.2576657132460.5364044932070.02918051231130.2071783932880.00024349683076-0.0893844454813-0.01349591074560.0279527621845-0.0475960714901-0.03803535699840.0209281289733-0.01583486793341.79955081593E-50.1993289290360.01575696459890.002213670532950.2471784438490.008969072185870.237282783536-13.074795338-0.28984956806325.5976059904
90.158753615933-0.09031860673660.09424507831390.08173166082810.02151312500070.09913342359120.08454957642740.00138671836427-0.164316928326-0.08795578456370.00842158830269-0.06197448548490.5254917502860.0238796816642-0.0009549366218050.3775269806080.03852679674130.0261485125470.251267028329-0.007343899782630.323471816905-15.3711133454-10.475236619318.4606523893
100.1497385405510.117362932220.03967764518030.155399143929-0.09857003091720.1676883962980.05145144763820.124165016085-0.125904904579-0.427871543569-0.0514436714815-0.06762287192660.39246938068-0.0329511885825-0.0008253835385160.513178596411-0.0700042990116-0.003491189984890.311247246404-0.007288887489070.348526331514-37.8582385618-25.24022872858.81201831388
110.02926623717-0.1157184196270.01561047695650.1704259550320.01676207494310.01340813302520.00454854059934-0.07033153015360.0479092403672-0.0622106121193-0.02574855459460.15470478960.277958245975-0.232545766419-4.30381962176E-50.52481071272-0.17444006591-0.07759975031180.3461650379270.07474064420040.400035904464-44.2163399944-27.44930139929.16785735807
120.618104436449-0.02837975480060.05541929776010.2987219527790.265922682240.220374095830.14469025921-0.0241613881001-0.0702944663805-0.3506809654740.03028582453540.3771796864020.344833095865-0.457442439470.0001484502315570.35854939557-0.125301517952-0.1040804251610.4207691921870.01788688345180.402380553646-51.4140756704-13.5940723317-0.0329268446287
130.0844295264543-0.0760508242781-0.0120794945050.2265073534910.1417064561860.2030294617150.158569709428-0.201827116827-0.0659174792646-0.0919789568245-0.2094299122730.182360757126-0.0791132297729-0.285047492244-0.003026590648980.248415582725-0.0752287906295-0.05136818969780.448769787505-0.01361640122690.385061616542-53.5608407472-6.74817319562.59343723328
140.0110503999061-0.01001268565520.01331271384650.07099531010450.1072151024580.47025267523-0.00671400320533-0.157792192926-0.02890462195030.0381587548761-0.2112383183020.268143629722-0.406758590547-0.202448510027-0.03003171265840.188637550115-0.007086243015990.01347901320410.412090461602-0.0322356454230.46789497688-55.6541769814-1.806181255979.20876818774
150.152122427245-0.01484473917930.1227080839420.04850373666530.04694628264660.2117750113460.0253480030003-0.0216406273504-0.0441439510366-0.011908969426-0.01507782119250.007843767180930.0322674953107-0.0727755370384-3.66167973052E-60.256695254173-0.03044457846070.01123262877920.2416596449720.005202888217410.259093840192-38.9123045539-4.1391936355510.9748396651
160.0203300036863-0.0123661853794-0.007690055801850.0193184003362-0.02268945228760.0355749459082-0.0663506405678-0.425846472215-0.1815833170350.210329900715-0.009930067795060.01961522948230.1876210707380.0372125733709-0.0001248449374460.246180580734-0.03617915162310.02439041922350.2972546639920.02472213887740.288349623759-38.4912327899-6.2293371658219.5086839544
170.02220482455450.0134231860864-0.0266899327070.00142000170987-0.01688770136290.0445122848383-0.1931671282720.309796175562-0.33755333167-0.1144599373590.04940851708890.007585818513350.3309978021810.0152677410118-0.0003339679457490.532294331561-0.01608706397390.02192741864390.378031907344-0.03426632168030.366624447694-30.19211063-14.9774726427-2.21561953353
180.1704918082160.1281774744450.04638821466290.125254439584-0.01374581886080.06290841425710.134176060832-0.187905977018-0.1973403011340.202975520415-0.138349043132-0.03831449894610.2852683153930.0178156575282-0.0006559174014360.359694742835-0.0221296329923-0.0261016880310.2506331127790.03829515269230.291594019694-30.9953904605-12.887272807520.6052541787
190.2284835098920.0489494598661-0.02815091821130.0331291387515-0.02528255012360.1076133921780.12149863949-0.1400548061210.312945793486-0.19001767787-0.176267593740.16934343985-0.420425976294-0.15643216406-0.0008953536380680.4293884470090.04474845144050.07681273106610.199595371417-0.08300425181070.393605635864-31.075610800931.394643666731.8905951857
200.0916814430295-0.00473466214386-0.1015510351290.235716007784-0.01288302236540.08237723344060.198993526548-0.1575563793980.395741648612-0.0386441864634-0.0397058315493-0.0840848630599-0.03201868299490.0859269831894-0.0001439065562750.3520087903890.06808450922480.01352734404010.34007506149-0.09324692441110.386784031535-35.394934729832.658102180636.8547626455
210.4172983528670.337761159329-0.02855352271480.2861999669770.04010214395870.151693688456-0.0465277339809-0.3346872259440.1559268053960.1707119556020.0324032638071-0.145908228352-0.101048884474-0.121741110289-4.24052985313E-50.3535198261380.0537564930703-0.004203081013620.389964749826-0.08740820121040.294895082869-30.188483484618.581028085947.1989169214
220.1639387668940.148073882875-0.05388540909010.144516441566-0.0332618646562-0.009489407461510.0566596027789-0.465812402804-0.08302809962720.333959789367-0.1641255629930.06177071502420.0635029634439-0.369445984809-0.004996905732860.3217023988450.03490685653180.03821542645490.646525094704-0.03912438149280.283935824866-36.574200579111.885547758452.3759527905
230.03786924114310.06142532350610.05473699949430.1179945772930.08070835713350.09043177191630.0620159464842-0.179973776219-0.003199352982030.0663806317808-0.0941249199762-0.0270460983668-0.137016359812-0.1651928107888.75580539335E-60.281636371290.01477647942860.0005475672479540.357580431801-0.03395543843480.260333218546-28.498233975310.916567114241.0250039759
240.0769993399707-0.04617521122960.1274364128820.1910136869880.07434335908750.185071031156-0.0626085426708-0.121924166805-0.08829859307750.0708734659837-0.03325702187-0.1072161542620.1112481432-0.1467647691046.23411583502E-50.251292620657-0.01251426160750.002263609397860.3126072873-0.006059787226960.23914427715-33.84542492678.0826003733438.9018022341
250.02743939952830.0129589393443-0.0425346201185-0.0088191770207-0.0214332874770.05098429026380.132854492919-0.05656691711670.03589990721710.111819330567-0.159770598321-0.0873348374106-0.08672636577420.04308243406339.78065942641E-50.2499842555110.0007784898241880.03002783103390.318641345943-0.02368075937460.256506156629-35.61910275477.3215018140931.7111876323
260.00629064960208-0.0183503905864-0.006436062894380.03806792135450.02675377486290.005592953692950.253515793270.1975899473580.10101533673-0.05048400971490.00143469870207-0.103469237845-0.2660511350890.105208430735-4.15908934458E-50.2873441708870.01106434461420.005646033623760.289643859524-0.01852381072790.305913776343-23.166356749614.771960297922.9005225851
270.06315416150450.001535305061530.04777447557950.0633721157915-0.06170686473170.07259209340590.00711412660054-0.1601028263240.0700991315402-0.0837784869149-0.02385639470330.276964518657-0.0668727894225-0.08985856492050.0003876681158830.2463500100160.02303681054650.0192316356110.28347225178-0.02596652079740.271135452065-37.287588874311.658824639124.8621226343
280.02580714144120.03829696211510.03379949027660.04375848223190.02967653774960.009916950883440.153821602420.08799765449930.355958625266-0.299608706481-0.172979904439-0.00531557572905-0.1533059865930.223445519564-0.0002999273807750.427296324153-0.05378953394550.008126814248480.3571393813-0.02393427700290.363918988882-16.23108019123.189401381331.5401842462
290.0680039481207-0.002513172194260.08521818098250.0784394321142-0.1037883156990.131786483866-0.0444087560970.04896352776370.0126729198212-0.331953467052-0.05455836636470.0797192810876-0.240200125761-0.03663034870937.38681367136E-50.331385490960.0485993804776-0.02517742970980.277732406782-0.04289906278340.310213580286-33.985548184619.529359758118.5056834543
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 66 )
2X-RAY DIFFRACTION2chain 'A' and (resid 67 through 237 )
3X-RAY DIFFRACTION3chain 'A' and (resid 238 through 260 )
4X-RAY DIFFRACTION4chain 'A' and (resid 261 through 283 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 57 )
6X-RAY DIFFRACTION6chain 'B' and (resid 58 through 156 )
7X-RAY DIFFRACTION7chain 'B' and (resid 157 through 184 )
8X-RAY DIFFRACTION8chain 'B' and (resid 185 through 260 )
9X-RAY DIFFRACTION9chain 'B' and (resid 261 through 283 )
10X-RAY DIFFRACTION10chain 'C' and (resid 1 through 29 )
11X-RAY DIFFRACTION11chain 'C' and (resid 30 through 57 )
12X-RAY DIFFRACTION12chain 'C' and (resid 58 through 116 )
13X-RAY DIFFRACTION13chain 'C' and (resid 117 through 156 )
14X-RAY DIFFRACTION14chain 'C' and (resid 157 through 171 )
15X-RAY DIFFRACTION15chain 'C' and (resid 172 through 218 )
16X-RAY DIFFRACTION16chain 'C' and (resid 219 through 237 )
17X-RAY DIFFRACTION17chain 'C' and (resid 238 through 260 )
18X-RAY DIFFRACTION18chain 'C' and (resid 261 through 284 )
19X-RAY DIFFRACTION19chain 'D' and (resid 1 through 29 )
20X-RAY DIFFRACTION20chain 'D' and (resid 30 through 57 )
21X-RAY DIFFRACTION21chain 'D' and (resid 58 through 116 )
22X-RAY DIFFRACTION22chain 'D' and (resid 117 through 137 )
23X-RAY DIFFRACTION23chain 'D' and (resid 138 through 156 )
24X-RAY DIFFRACTION24chain 'D' and (resid 157 through 184 )
25X-RAY DIFFRACTION25chain 'D' and (resid 185 through 204 )
26X-RAY DIFFRACTION26chain 'D' and (resid 205 through 218 )
27X-RAY DIFFRACTION27chain 'D' and (resid 219 through 237 )
28X-RAY DIFFRACTION28chain 'D' and (resid 238 through 260 )
29X-RAY DIFFRACTION29chain 'D' and (resid 261 through 283 )

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