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- PDB-8xfr: Structure of the alginate epimerase/lyase complexed with tetra-ma... -

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Basic information

Entry
Database: PDB / ID: 8xfr
TitleStructure of the alginate epimerase/lyase complexed with tetra-mannuronic acid
Componentsmannuronan 5-epimerase
KeywordsISOMERASE / Substrate / Complex / Epimerase
Function / homology
Function and homology information


mannuronan 5-epimerase / alginic acid biosynthetic process / isomerase activity / lyase activity / calcium ion binding / extracellular region
Similarity search - Function
Carbohydrate-binding/sugar hydrolysis domain / Pectate lyase superfamily protein / Pectate lyase superfamily protein / Domain present in carbohydrate binding proteins and sugar hydrolses / Hemolysin-type calcium-binding conserved site / Hemolysin-type calcium-binding region signature. / RTX calcium-binding nonapeptide repeat / RTX calcium-binding nonapeptide repeat (4 copies) / Parallel beta-helix repeat / Parallel beta-helix repeats ...Carbohydrate-binding/sugar hydrolysis domain / Pectate lyase superfamily protein / Pectate lyase superfamily protein / Domain present in carbohydrate binding proteins and sugar hydrolses / Hemolysin-type calcium-binding conserved site / Hemolysin-type calcium-binding region signature. / RTX calcium-binding nonapeptide repeat / RTX calcium-binding nonapeptide repeat (4 copies) / Parallel beta-helix repeat / Parallel beta-helix repeats / Serralysin-like metalloprotease, C-terminal / Pectin lyase fold / Pectin lyase fold/virulence factor
Similarity search - Domain/homology
ACETATE ION / DI(HYDROXYETHYL)ETHER / mannuronan 5-epimerase
Similarity search - Component
Biological speciesAzotobacter chroococcum NCIMB 8003 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFujiwara, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)21K06077 Japan
CitationJournal: Febs Lett. / Year: 2024
Title: Structural basis for the minimal bifunctional alginate epimerase AlgE3 from Azotobacter chroococcum.
Authors: Fujiwara, T. / Mano, E. / Nango, E.
History
DepositionDec 14, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 15, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: mannuronan 5-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,32314
Polymers51,7491
Non-polymers1,57513
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-12 kcal/mol
Surface area17960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.584, 121.584, 117.617
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein mannuronan 5-epimerase


Mass: 51748.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter chroococcum NCIMB 8003 (bacteria)
Gene: algE7, Achr_39570 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0C4WKK2, mannuronan 5-epimerase
#2: Polysaccharide beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid- ...beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid


Type: oligosaccharide / Mass: 722.510 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpAb1-4DManpAb1-4DManpAb1-4DManpAb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a1122A-1b_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][b-D-ManpA]{[(4+1)][b-D-ManpA]{[(4+1)][b-D-ManpA]{[(4+1)][b-D-ManpA]{}}}}LINUCSPDB-CARE

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Non-polymers , 5 types, 150 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 3.23 Å3/Da / Density % sol: 61.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M sodium acetate, pH4.5, 30% w/v PEG 4000, 15% v/v glycerol

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→48.05 Å / Num. obs: 43816 / % possible obs: 100 % / Redundancy: 24.1 % / Biso Wilson estimate: 45.43 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.096 / Net I/σ(I): 20.97
Reflection shellResolution: 2→2.14 Å / Redundancy: 24.4 % / Rmerge(I) obs: 1.926 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 8053 / CC1/2: 0.858 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.19.2_4158phasing
PHENIX1.19.2_4158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→48.05 Å / SU ML: 0.1946 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 21.712
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1865 2204 5.03 %
Rwork0.1624 41591 -
obs0.1635 43795 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.56 Å2
Refinement stepCycle: LAST / Resolution: 2→48.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3604 0 94 138 3836
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00973756
X-RAY DIFFRACTIONf_angle_d1.03745072
X-RAY DIFFRACTIONf_chiral_restr0.0683552
X-RAY DIFFRACTIONf_plane_restr0.0076694
X-RAY DIFFRACTIONf_dihedral_angle_d8.3878573
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.040.29931060.25562630X-RAY DIFFRACTION99.89
2.04-2.090.28741580.23022558X-RAY DIFFRACTION99.96
2.09-2.140.28021410.22362642X-RAY DIFFRACTION100
2.14-2.20.20571400.22545X-RAY DIFFRACTION99.93
2.2-2.270.23421530.19322597X-RAY DIFFRACTION100
2.27-2.340.21281340.18042647X-RAY DIFFRACTION100
2.34-2.420.24421380.18392570X-RAY DIFFRACTION100
2.42-2.520.23611320.17192617X-RAY DIFFRACTION99.93
2.52-2.630.24211240.19612614X-RAY DIFFRACTION99.96
2.63-2.770.21331370.18632607X-RAY DIFFRACTION99.93
2.77-2.950.21911620.19682540X-RAY DIFFRACTION100
2.95-3.170.19641400.17572613X-RAY DIFFRACTION100
3.17-3.490.21121690.17632587X-RAY DIFFRACTION100
3.49-40.17481180.1442598X-RAY DIFFRACTION100
4-5.040.14531180.12662638X-RAY DIFFRACTION99.86
5.04-48.050.13281340.14592588X-RAY DIFFRACTION99.85
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)
10.4533510186310.1141069588030.2706433383421.065618304390.6465172706730.723276863310.08202654930930.4276892662640.235291210301-0.863405893394-0.24440328502-0.418658221801-0.3740534239320.303545630633-0.1765285710310.989029543978-0.001550749371180.3611293573920.8798044667110.2380014731910.78052500054734.380535772410.7151144967-64.1817190394
20.5859194868840.0492420280187-0.3330704696381.082491959010.1261207115581.135476497370.2631413858470.5767644349850.279864742598-0.42557042582-0.172930778229-0.538632076065-0.5910636751080.3408602122030.05720989090010.873113511131-0.009880230926390.2892704983640.6660557401140.1688809860950.70980108797730.1316158549.71956969489-56.487779212
30.4895418590740.1061425959890.05371969514131.28058061672-0.1487956139521.797344387740.2565343602730.4098672267480.279174901347-0.348885224496-0.102689300559-0.117473522136-0.3978381119270.06086251491844.84012028601E-50.6252215956660.09851794607280.1607300562430.5751623706090.06892683740860.55401485710722.74657036592.87078784613-53.1980969092
40.7643055734540.0790114335818-0.660644211471.1602400201-0.7021491354792.854440853810.2759596111620.03941248138210.156880045423-0.084395193699-0.163758293296-0.385810065263-0.334538120710.2867424306552.36600231674E-50.423831880616-0.02108528298680.06523270198360.42147622787-0.02000273273160.50507951570224.709422873-0.0724096989325-40.9805676245
50.189800572034-0.107826031064-0.5130365904410.52307107412-0.4729855557691.71744086760.03915796596710.2397799841510.0967055955711-0.168294792073-0.0561936910925-0.18081153676-0.213068526620.106515719081-3.06199151935E-50.375526401556-0.00485288500898-0.02347124884480.391296287304-0.04465355554660.48231673281217.8768251307-7.10044637539-34.0098404094
61.2191070712-0.200974989142-0.6585831915851.22631523108-0.7455436376931.971181684820.115654769876-0.107359142261-0.03666957821180.231794515334-0.0548813857721-0.0608654011283-0.09026174149220.1837066887260.0001285857462660.399023689928-0.0200547215957-0.06208246400180.409576914329-0.05472131171490.43229791545216.7589008406-8.28343400282-24.9330550082
70.575616748943-0.335010368118-0.5993224632090.813011729802-0.7065666905221.7897795905-0.0990077639344-0.122336278437-0.1526440316890.2816342095270.0523052818094-0.06958189279860.0162532808930.163948647674-5.15294890674E-50.563047578146-0.0197764276833-0.1079400222350.470434913336-0.006089528399730.49502895372416.5776684049-16.8262391155-14.9820160545
80.424864045280.266342159483-0.5700177701870.518017787066-0.8006998730871.14786816196-0.0494963140482-0.227934509729-0.598223353508-0.0340655640925-0.00911590068697-0.09950889083190.583658407018-0.0056378948985-0.0001207538098760.700723069838-0.0278134593053-0.05640037580650.4600640866630.0369657861730.63548674274111.3488900262-28.8268492006-11.5534054491
91.211315221821.28671746017-0.5874275750241.30067419277-1.252615592951.886930876070.116306972453-0.251371615514-0.1471454832720.24682814978-0.1395567849990.0905029381569-0.06736722160130.172178671513-6.55199908677E-50.6795343622030.0218617819433-0.01270604614650.4568272469280.0673601235790.4700051064518.70720092907-25.2826765119-3.18695376751
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 1 through 31 )1 - 311 - 31
22chain 'A' and (resid 32 through 82 )32 - 8232 - 82
33chain 'A' and (resid 83 through 139 )83 - 13983 - 139
44chain 'A' and (resid 140 through 224 )140 - 224140 - 224
55chain 'A' and (resid 225 through 259 )225 - 259225 - 259
66chain 'A' and (resid 260 through 326 )260 - 326260 - 326
77chain 'A' and (resid 327 through 376 )327 - 376327 - 376
88chain 'A' and (resid 377 through 402 )377 - 402377 - 402
99chain 'A' and (resid 403 through 480 )403 - 480403 - 480

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