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- PDB-8ja4: Structure of the alginate epimerase/lyase -

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Basic information

Entry
Database: PDB / ID: 8ja4
TitleStructure of the alginate epimerase/lyase
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
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
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / mannuronan 5-epimerase
Similarity search - Component
Biological speciesAzotobacter chroococcum NCIMB 8003 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 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 5, 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

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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)53,54412
Polymers52,6841
Non-polymers85911
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-12 kcal/mol
Surface area17990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.520, 122.520, 119.800
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

#1: Protein mannuronan 5-epimerase


Mass: 52684.410 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: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C4H10O3
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 3.29 Å3/Da / Density % sol: 62.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M sodium acetate, pH4.5-pH4.9, 24-30% w/v PEG 4000, 15% v/v glycerol

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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: Oct 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.04→48.51 Å / Num. obs: 42695 / % possible obs: 100 % / Redundancy: 12 % / Biso Wilson estimate: 48.15 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.018 / Rrim(I) all: 0.062 / Net I/σ(I): 22.19
Reflection shellResolution: 2.04→2.11 Å / Redundancy: 12.1 % / Rmerge(I) obs: 1.231 / Mean I/σ(I) obs: 1.83 / Num. unique obs: 4254 / CC1/2: 0.803 / CC star: 0.944 / Rpim(I) all: 0.37 / Rrim(I) all: 1.286 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.04→48.51 Å / SU ML: 0.2198 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 18.145
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1721 2112 4.95 %
Rwork0.1671 40566 -
obs0.1674 42678 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60 Å2
Refinement stepCycle: LAST / Resolution: 2.04→48.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3594 0 47 163 3804
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01513722
X-RAY DIFFRACTIONf_angle_d1.63765027
X-RAY DIFFRACTIONf_chiral_restr0.081537
X-RAY DIFFRACTIONf_plane_restr0.0108696
X-RAY DIFFRACTIONf_dihedral_angle_d11.2054556
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.04-2.110.28172040.26314050X-RAY DIFFRACTION100
2.11-2.20.22852150.21424091X-RAY DIFFRACTION100
2.2-2.30.21481790.18984046X-RAY DIFFRACTION100
2.3-2.420.19681860.18134110X-RAY DIFFRACTION100
2.42-2.570.20612770.19543974X-RAY DIFFRACTION100
2.57-2.770.24571870.20844085X-RAY DIFFRACTION100
2.77-3.050.19012220.19984057X-RAY DIFFRACTION100
3.05-3.490.19662240.18554058X-RAY DIFFRACTION100
3.49-4.390.1532050.14394041X-RAY DIFFRACTION99.98
4.39-48.510.12982130.13764054X-RAY DIFFRACTION99.56
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)
10.0145920869760.0009873914758610.006899242490890.00154771949193-0.0125363149196-0.00588953970019-0.05299670934270.22144160111-0.288039760874-0.0813104585963-0.06031560416310.03732578188040.208032423638-0.11501124837-0.137855123230.7863483521260.0990299598469-0.02064027078011.13142360347-0.6428592065710.917538185762-8.35819897716-34.9487580977-24.6597796343
20.04299493674240.0290150629229-0.05248223147980.127535557327-0.1254360864670.170063232411-0.006641649057550.663055989847-0.773450774268-0.3960679961580.0866068676429-0.09739949127340.5975595197670.207352717406-0.08457685585080.5785593619530.157975649041-0.02504313110420.837358645452-0.7640048976970.815175153259-6.91758099483-30.7888877905-17.1291416194
30.0669580889313-0.0498254367162-0.1027885693920.1035278799310.04755933910930.1276049736910.07423257341580.776723909135-0.526735653129-0.1338867551670.130078713588-0.09811267183620.08568337202550.2458935081730.0003429684035820.4981066670160.0386994125898-0.01780842268160.777282375915-0.2695138208070.639938785325-9.01152442734-20.9265439934-13.7130128195
40.1758488159750.00507931944736-0.0605467965080.08660910766770.1711583508490.2705483652620.1041703473940.388345255371-0.4816384545460.07331225389760.05575136427230.02134542731680.1140341589810.05450290185682.08113685764E-50.4184741951490.00934658974166-0.05549558883340.431010249655-0.1303683902250.562393273067-13.0081717079-21.260287518-1.61557220698
50.009552174014790.02205411469580.01760244943620.02313977100810.03499369857580.091261753335-0.005488134740580.249763521305-0.2885516194670.00692182958699-0.00717654373666-0.1054116339450.04369896051590.1027795121753.79971761512E-80.445860759530.00810262833969-0.01479968407670.398184953205-0.003954228930320.498225683015-15.3634621899-11.73229630035.43626883829
60.184608551715-0.0178157201972-0.1142267222720.1187927457420.20229969080.35105314542-0.00155488481828-0.109546967122-0.1131776947340.2410140797260.072731470293-0.1229623327030.0638268249306-0.06284700332756.3704512005E-50.416539365199-0.0207683494223-0.0256256155680.3598714327050.05742429496020.449968818524-16.0844987101-10.297914635814.4180920417
70.0880406430566-0.00267278436765-0.02593212836820.04518748747160.06843914754640.0509297454148-0.0240547910244-0.2027953854350.02391507767820.08467565195950.102812979470.06044828903120.0237498574767-0.149954258343-3.47216466294E-50.5042549873020.005807428291510.0392748877570.4958837976930.09859568675160.463191392263-23.3956399583-5.6207350961924.2514585539
80.0332782037457-0.0493606022724-0.07497265614890.03512696142340.06112654079410.07991049788170.0749482119456-0.4062963736580.2327831897-0.01078646306230.03293559410320.198536922488-0.151342082944-0.4764473590885.20005941567E-50.5311561732240.07386263045140.07585060968860.5824609774150.05410778558320.442333029546-31.2366862544.682926957528.2125317698
90.131288571104-0.0252774599379-0.05149369195220.19163941140.2033726623940.1661688003210.00492421277484-0.2269436803330.1424055133290.2113239228160.09043327576170.0215347384133-0.0211612841502-0.0460271341991-1.9727550848E-50.5358037785380.08827513752850.07682316362710.637099560327-0.01006570329510.452898950607-26.97756090124.9816811222936.3907343259
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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