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- PDB-6kfn: Crystal structure of alginate lyase from Paenibacillus sp. str. FPU-7 -

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Basic information

Entry
Database: PDB / ID: 6kfn
TitleCrystal structure of alginate lyase from Paenibacillus sp. str. FPU-7
Componentsalginate lyase
KeywordsLYASE / alginate lyase
Function / homologyIMIDAZOLE
Function and homology information
Biological speciesPaenibacillus sp. FPU-7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 0.89 Å
AuthorsItoh, T. / Nakagawa, E. / Yoda, M. / Nakaichi, A. / Hibi, T. / Kimoto, H.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science16K08114 Japan
Japan Society for the Promotion of Science19K06340 Japan
CitationJournal: Sci Rep / Year: 2019
Title: Structural and biochemical characterisation of a novel alginate lyase from Paenibacillus sp. str. FPU-7.
Authors: Itoh, T. / Nakagawa, E. / Yoda, M. / Nakaichi, A. / Hibi, T. / Kimoto, H.
History
DepositionJul 8, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: alginate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4414
Polymers32,3261
Non-polymers1153
Water7,800433
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-12 kcal/mol
Surface area10980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.635, 57.764, 39.714
Angle α, β, γ (deg.)90.000, 91.100, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein alginate lyase


Mass: 32325.549 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus sp. FPU-7 (bacteria) / Production host: Escherichia coli (E. coli) / References: mannuronate-specific alginate lyase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 433 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.32 Å3/Da / Density % sol: 46.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG8000, imidazole

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.85 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: May 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.85 Å / Relative weight: 1
ReflectionResolution: 0.89→50 Å / Num. obs: 200667 / % possible obs: 92.6 % / Redundancy: 4.4 % / Biso Wilson estimate: 5.3 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 29.5
Reflection shellResolution: 0.89→0.91 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.672 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 9592 / % possible all: 88.5

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 0.89→23.357 Å / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 11.15
RfactorNum. reflection% reflection
Rfree0.1216 9974 4.97 %
Rwork0.1052 --
obs0.106 200667 92.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 130.77 Å2 / Biso mean: 11.8909 Å2 / Biso min: 0.01 Å2
Refinement stepCycle: final / Resolution: 0.89→23.357 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2192 0 11 436 2639
Biso mean--22.42 27.82 -
Num. residues----298
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
0.89-0.89980.21493570.2107604488
0.8998-0.91030.19183230.1938605389
0.9103-0.92140.19012880.181612189
0.9214-0.93310.16683350.1762604089
0.9331-0.94540.19093180.1604615289
0.9454-0.95830.16853240.1527606289
0.9583-0.9720.15233280.1457614189
0.972-0.98650.17383090.1399608490
0.9865-1.0020.14363120.1256624890
1.002-1.01840.14012970.1221619490
1.0184-1.03590.13192940.1125614790
1.0359-1.05480.12173360.1075620591
1.0548-1.07510.12283580.1019622591
1.0751-1.0970.1293380.1006626691
1.097-1.12090.10573200.1015630292
1.1209-1.14690.11433720.0996633593
1.1469-1.17560.12012920.0984642193
1.1756-1.20740.10683330.096642894
1.2074-1.24290.10153450.0938641694
1.2429-1.2830.10443420.0886651495
1.283-1.32890.10713610.0877649195
1.3289-1.38210.11063390.0887653295
1.3821-1.4450.10053320.0878661596
1.445-1.52120.10663360.086666596
1.5212-1.61640.09383620.082662897
1.6164-1.74120.10633720.0921669697
1.7412-1.91640.10463810.0945670898
1.9164-2.19350.10183470.0879678498
2.1935-2.76290.11782980.0986690699
2.7629-23.3570.14653250.1217627089

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