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- PDB-7c8f: Structure of alginate lyase AlyC3 in complex with dimannuronate(2M) -

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Basic information

Entry
Database: PDB / ID: 7c8f
TitleStructure of alginate lyase AlyC3 in complex with dimannuronate(2M)
ComponentsH127A/Y244A mutant of alginate lyase AlyC3 in complex with dimannuronate
KeywordsLYASE / alginate / alginate lyase
Function / homologyMALONATE ION
Function and homology information
Biological speciesPsychromonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.461 Å
AuthorsZhang, Y.Z. / Xu, F. / Chen, X.L. / Wang, P.
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Structural and molecular basis for the substrate positioning mechanism of a new PL7 subfamily alginate lyase from the arctic.
Authors: Xu, F. / Chen, X.L. / Sun, X.H. / Dong, F. / Li, C.Y. / Li, P.Y. / Ding, H. / Chen, Y. / Zhang, Y.Z. / Wang, P.
History
DepositionMay 30, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 2.0Oct 14, 2020Group: Atomic model / Data collection / Derived calculations
Category: atom_site / pdbx_nonpoly_scheme ...atom_site / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_oper_list
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_nonpoly_scheme.auth_seq_num
Revision 2.1Dec 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 2.2Nov 29, 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

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Assembly

Deposited unit
A: H127A/Y244A mutant of alginate lyase AlyC3 in complex with dimannuronate
B: H127A/Y244A mutant of alginate lyase AlyC3 in complex with dimannuronate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4856
Polymers60,5412
Non-polymers9454
Water13,763764
1
B: H127A/Y244A mutant of alginate lyase AlyC3 in complex with dimannuronate
hetero molecules

A: H127A/Y244A mutant of alginate lyase AlyC3 in complex with dimannuronate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4856
Polymers60,5412
Non-polymers9454
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_445x-1/2,y-1/2,z1
Unit cell
Length a, b, c (Å)80.865, 106.413, 79.293
Angle α, β, γ (deg.)90.000, 93.850, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein H127A/Y244A mutant of alginate lyase AlyC3 in complex with dimannuronate


Mass: 30270.254 Da / Num. of mol.: 2 / Mutation: H127A, Y244A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Psychromonas sp. (bacteria) / Production host: Escherichia coli (E. coli)
#2: Polysaccharide beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid


Type: oligosaccharide / Mass: 370.263 Da / Num. of mol.: 2
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-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C3H2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 764 / 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: 2.81 Å3/Da / Density % sol: 56.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-Tris propane (pH 7.5), 0.2 M sodium malonate, and 19% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.46→50 Å / Num. obs: 113418 / % possible obs: 98.2 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 40.77
Reflection shellResolution: 1.46→1.49 Å / Rmerge(I) obs: 0.291 / Num. unique obs: 5754

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7C8G

7c8g


Resolution: 1.461→30.353 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 17.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1724 5589 4.93 %
Rwork0.1556 107816 -
obs0.1564 113405 98.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 117.88 Å2 / Biso mean: 25.7688 Å2 / Biso min: 8.1 Å2
Refinement stepCycle: final / Resolution: 1.461→30.353 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4264 0 68 764 5096
Biso mean--50.13 37.89 -
Num. residues----532
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064479
X-RAY DIFFRACTIONf_angle_d0.9676053
X-RAY DIFFRACTIONf_chiral_restr0.092656
X-RAY DIFFRACTIONf_plane_restr0.005789
X-RAY DIFFRACTIONf_dihedral_angle_d16.7661657
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.461-1.47730.22981780.2104352796
1.4773-1.49470.23132090.20923639100
1.4947-1.51290.23781910.19813606100
1.5129-1.53210.23221880.19653633100
1.5321-1.55220.22050.18433646100
1.5522-1.57350.18491890.1738358999
1.5735-1.5960.1791830.1742366199
1.596-1.61980.19291810.1715364999
1.6198-1.64510.17031890.1681359799
1.6451-1.67210.22191830.1701365299
1.6721-1.70090.19741730.1723360899
1.7009-1.73180.20581690.1656357098
1.7318-1.76520.19471900.1697349896
1.7652-1.80120.20411830.1705337592
1.8012-1.84030.20641760.1797361899
1.8403-1.88310.20851670.1777365599
1.8831-1.93020.19172010.1669360399
1.9302-1.98240.18922110.1657362899
1.9824-2.04070.19512150.162359499
2.0407-2.10660.17751980.1647360399
2.1066-2.18190.16822260.1609356699
2.1819-2.26920.15091990.1542360298
2.2692-2.37240.15871810.1595357497
2.3724-2.49740.17971590.1617343493
2.4974-2.65380.17081790.1614351796
2.6538-2.85860.15351750.1593657100
2.8586-3.1460.16041800.1549365399
3.146-3.60060.16211730.1379366699
3.6006-4.5340.14761650.1201360497
4.534-30.3530.1521730.1433359295

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