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- PDB-8jaz: Structure of the alginate epimerase/lyase complexed with di-mannu... -

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Basic information

Entry
Database: PDB / ID: 8jaz
TitleStructure of the alginate epimerase/lyase complexed with di-mannuronic acid
Componentsmannuronan 5-epimerase
KeywordsISOMERASE / bifunctional epimerase/lyase
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
Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Carbohydrate-binding/sugar hydrolysis domain / 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 ...Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Carbohydrate-binding/sugar hydrolysis domain / 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
mannuronan 5-epimerase
Similarity search - Component
Biological speciesAzotobacter chroococcum NCIMB 8003 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 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
DepositionMay 7, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 8, 2024Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jun 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
B: mannuronan 5-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,63916
Polymers105,7472
Non-polymers89114
Water13,205733
1
A: mannuronan 5-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1548
Polymers52,8741
Non-polymers2817
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18120 Å2
MethodPISA
2
B: mannuronan 5-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4848
Polymers52,8741
Non-polymers6117
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-12 kcal/mol
Surface area18340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.330, 40.030, 188.290
Angle α, β, γ (deg.)90.000, 91.450, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 83 or resid 85...
d_2ens_1(chain "B" and (resid 1 through 83 or resid 85...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11METMETGLNGLNAA1 - 831 - 83
d_12LEULEUTHRTHRAA85 - 25785 - 257
d_13ASNASNASPASPAA259 - 437259 - 437
d_14ALAALALEULEUAA440 - 479440 - 479
d_15CACACACAAD501
d_16CACACACAAE502
d_17CACACACAAF503
d_18CACACACAAG504
d_19CACACACAAH505
d_21METMETGLNGLNBB1 - 831 - 83
d_22LEULEUTHRTHRBB85 - 25785 - 257
d_23ASNASNASPASPBB259 - 437259 - 437
d_24ALAALALEULEUBB440 - 479440 - 479
d_25CACACACABK501
d_26CACACACABL502
d_27CACACACABM503
d_28CACACACABN504
d_29CACACACABO505

NCS oper: (Code: givenMatrix: (0.997380205705, -0.0580732008061, -0.0431303676782), (-0.0603361454158, -0.996761359879, -0.0531633427145), (-0.039903318462, 0.0556263858286, -0.997653963243)Vector: ...NCS oper: (Code: given
Matrix: (0.997380205705, -0.0580732008061, -0.0431303676782), (-0.0603361454158, -0.996761359879, -0.0531633427145), (-0.039903318462, 0.0556263858286, -0.997653963243)
Vector: 24.0918876546, -2.48056974706, -95.1406314425)

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Components

#1: Protein mannuronan 5-epimerase


Mass: 52873.734 Da / Num. of mol.: 2
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


Type: oligosaccharide / Mass: 370.263 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpAb1-4DManpAb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a1122A-1b_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-ManpA]{[(4+1)][b-D-ManpA]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 733 / 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: 2.19 Å3/Da / Density % sol: 43.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.15-0.25M calcium chloride, 16-22% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.82→47.06 Å / Num. obs: 80215 / % possible obs: 98.29 % / Redundancy: 8 % / CC1/2: 0.986 / CC star: 0.997 / Rmerge(I) obs: 0.1873 / Rpim(I) all: 0.0647 / Rrim(I) all: 0.199 / Net I/σ(I): 8.41
Reflection shellResolution: 1.82→1.885 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.3867 / Mean I/σ(I) obs: 2.29 / Num. unique obs: 7256 / CC1/2: 0.78 / CC star: 0.936 / Rpim(I) all: 0.1763 / Rrim(I) all: 0.428 / % possible all: 90.32

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.82→47.06 Å / Cross valid method: FREE R-VALUE / σ(F): 1.65 / Phase error: 29.1802
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2436 4307 5.37 %
Rwork0.2166 75908 -
obs0.2242 80215 98.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.13 Å2
Refinement stepCycle: LAST / Resolution: 1.82→47.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7196 0 38 733 7967
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00247337
X-RAY DIFFRACTIONf_angle_d0.60949917
X-RAY DIFFRACTIONf_chiral_restr0.0471069
X-RAY DIFFRACTIONf_plane_restr0.01381358
X-RAY DIFFRACTIONf_dihedral_angle_d10.96871124
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.46882021185 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.850.26871780.26183326X-RAY DIFFRACTION83.86
1.85-1.890.27562140.2513538X-RAY DIFFRACTION86.95
1.89-1.920.27362290.24343610X-RAY DIFFRACTION89.49
1.92-1.960.26322150.24083698X-RAY DIFFRACTION91.63
1.96-20.23642060.24833851X-RAY DIFFRACTION93.7
2-2.050.25242040.23833733X-RAY DIFFRACTION94.01
2.05-2.10.30852100.24163822X-RAY DIFFRACTION93.86
2.1-2.160.2782070.24253785X-RAY DIFFRACTION93.9
2.16-2.220.2842550.2393816X-RAY DIFFRACTION93.12
2.22-2.290.25061840.24143799X-RAY DIFFRACTION94.95
2.29-2.370.27231970.23343883X-RAY DIFFRACTION94.82
2.37-2.470.23291880.2313848X-RAY DIFFRACTION94.97
2.47-2.580.26942070.23013883X-RAY DIFFRACTION94.71
2.58-2.720.25072420.22833828X-RAY DIFFRACTION94.01
2.72-2.890.24052210.22043876X-RAY DIFFRACTION94.54
2.89-3.110.24251730.22233921X-RAY DIFFRACTION95.7
3.11-3.420.22972210.21683867X-RAY DIFFRACTION94.59
3.43-3.920.23542280.20333895X-RAY DIFFRACTION94.47
3.92-4.940.22572210.18863938X-RAY DIFFRACTION94.41
4.94-47.060.2371960.20824102X-RAY DIFFRACTION95.13
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)
10.003080954482270.0010569220977-0.000143944303582-0.0001449902060640.001027578516340.002616393800450.004131176782120.00855596898474-0.00148908296276-0.00456490751304-0.002270807019340.001809081579220.000811846588627-0.003156826267080.01154226433530.02058272898870.01140609987980.03722417144050.131152025499-0.00456359578341-0.0291524393171-13.97401738914.54585399389-111.013246169
20.005271401104080.00291140354941-0.007084108450730.00135114883941-0.003264412854830.00858156472403-0.00676951610168-0.000941277119992-0.00427718063524-0.00306391385237-0.00210495793677-0.003979393025770.0109857907272-0.000928821848732-0.009534817910470.06886751030360.01209429656030.01811039928810.09508612040510.001321547897920.00746221715906-7.801351782282.43329924116-99.7110796641
30.001118248347780.0008045593714990.00430528006080.00197495856481-0.001400959292990.0143988478546-0.00426902453235-0.00613488472981-0.0015964092790.001736117426-0.00449787086609-0.00538560158401-0.00380167336071-0.00521574442912-0.04193754440440.01155239186280.005000285874910.03272070458330.1450464902860.0117632753211-0.0756509411697-14.72833954254.10817572737-86.972871495
40.004576022517310.000573967509838-0.00165033140368-0.0001467231971990.001785687881950.008495890663850.000659864605944-0.00263549416629-0.002385886937310.0008697588921130.001249409011743.60228088817E-50.00182147568489-0.01293519326610.007759933695940.028090788355-0.00333052038543-0.00241298454280.1205793427680.0122874758736-0.00183547845675-12.48676929540.0910798605923-70.9216345534
50.00471302510348-0.00169579201364-0.006805195788180.00184038002901-0.0005971302025490.0240207467955-0.00799485287040.009592427495460.004497660530450.00859802706409-0.007967877639960.000990371506298-0.000908891908721-0.0045852816513-0.06685201083390.0874101242314-0.006735017320840.0009093799527480.216124518314-0.0023540260512-0.0119014444768-14.10612566218.41380996385-51.306889792
60.001354094444090.000324509867910.00152087329778-0.0001660902822030.0002215221837230.00147641376501-0.00346498987665-0.0008441575630456.42189831293E-50.00605689309969-0.002636787246420.002956634972720.016999061947-0.00983136593337-0.007740199088710.101818446509-0.00998986862127-0.002936738721760.156378251557-0.007010860648640.0297315833325-14.12729108545.90167783586-43.6242321126
77.13301937822E-5-0.0005118717926760.0004940679136750.00187023202219-0.001694783679230.00182347640234-0.00304337894654-0.005416744014790.0001148127149720.00430984568205-0.004579320823540.000419461700989-0.001090894610060.00126870565075-0.01347788926570.08882669695240.00539631430293-0.002328477026090.149386296914-0.003768943707110.01324999474312.0712451325-1.7000327816722.378198978
8-0.000310041007163-0.003472886908387.23496368555E-50.004225275066239.90353460718E-50.005323928783060.00324444637921-0.004267448427480.0003527353696710.003238250617590.00168321253505-0.00752078056986-0.003558474555430.005100511341490.03484453612780.0175794506974-0.0142226667637-0.0004267276062420.133456169090.000276264846904-0.091103513446715.94829791290.2017381738324.68654547488
90.00133990616479-0.000863913840422-0.00412920696252-0.00180392823544-0.0001999078812850.01232718787960.005453445019530.005930752182390.00231937181521-0.001886149833670.00552147923336-0.00157927037706-0.00519839283563-0.01300085113310.0581597631750.04568242293780.001254530905780.004289505456480.185352276970.00395769550652-0.036624181260113.22925040490.10902953344-18.6335398561
100.00307154778259-0.000625582517706-0.003813424822620.002688502098480.005140533626470.0125932313743-0.00594752908519-0.00482719130965-0.001864438399940.002056771598750.00145333531478-0.00238907893265-0.00826439644488-0.010424197851-0.01397745313580.07735842146810.01958541617880.0004351468766780.172721106242-0.009321243563190.0062494001225311.4067547474-5.83960202348-36.5674847841
113.80652130518E-5-0.000884154631906-0.0003863373893920.003672516097640.003245401648940.00279701283631-0.003906672580790.00329382533128-0.00350663537432-0.0104193716887-0.00188977239027-0.00094617256720.0125261719642-0.00651646931606-0.007113658566190.07657759364980.02009724868110.01247382608450.174608144234-0.01204224366210.014927282613813.6949526426-10.4956345698-50.9873168598
120.000310606200182-1.90852543208E-5-8.82884477775E-5-1.1855713004E-55.98342175889E-64.19041950659E-7-0.0003254238654950.00106352098736-0.000234050791734-0.00176841673947-0.001942384768350.000674682346634-0.01123875567270.00165878258147-0.003468873193450.116520817860.01243167650650.02008879601290.159218049750.009905736562120.03498609700127.225812072062.33346823816-49.5917243414
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 108 )AA1 - 1081 - 108
22chain 'A' and (resid 109 through 139 )AA109 - 139109 - 139
33chain 'A' and (resid 140 through 268 )AA140 - 268140 - 268
44chain 'A' and (resid 269 through 322 )AA269 - 322269 - 322
55chain 'A' and (resid 323 through 430 )AA323 - 430323 - 430
66chain 'A' and (resid 431 through 479 )AA431 - 479431 - 479
77chain 'B' and (resid 1 through 46 )BI1 - 461 - 46
88chain 'B' and (resid 47 through 206 )BI47 - 20647 - 206
99chain 'B' and (resid 207 through 322 )BI207 - 322207 - 322
1010chain 'B' and (resid 323 through 383 )BI323 - 383323 - 383
1111chain 'B' and (resid 384 through 452 )BI384 - 452384 - 452
1212chain 'B' and (resid 453 through 479 )BI453 - 479453 - 479

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