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Basic information

Entry
Database: PDB / ID: 6jp4
TitleCrystal structure of the catalytic domain of a multi-domain alginate lyase Dp0100 from thermophilic bacterium Defluviitalea phaphyphila
ComponentsAlginate lyase
KeywordsLYASE / alpha barrel+beta sandwich
Function / homology
Function and homology information


mannuronate-specific alginate lyase / poly(beta-D-mannuronate) lyase activity / hydrolase activity, acting on glycosyl bonds / metabolic process / carbohydrate binding / metal ion binding
Similarity search - Function
Heparinase II, N-terminal / Domain of unknown function (DUF4962) / Heparinase II/III-like / Heparinase II/III-like protein / Alginate lyase / Chondroitin AC/alginate lyase / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain ...Heparinase II, N-terminal / Domain of unknown function (DUF4962) / Heparinase II/III-like / Heparinase II/III-like protein / Alginate lyase / Chondroitin AC/alginate lyase / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Galactose-binding-like domain superfamily / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
ACETATE ION / CACODYLATE ION / : / Alginate lyase
Similarity search - Component
Biological speciesDefluviitalea phaphyphila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.069 Å
AuthorsJi, S.Q. / Dix, S.R. / Aziz, A. / Sedelnikova, S.E. / Li, F.L. / Rice, D.W.
Funding support China, United Kingdom, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31670001 China
Royal Society170392 United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2019
Title: The molecular basis of endolytic activity of a multidomain alginate lyase fromDefluviitalea phaphyphila, a representative of a new lyase family, PL39.
Authors: Ji, S. / Dix, S.R. / Aziz, A.A. / Sedelnikova, S.E. / Baker, P.J. / Rafferty, J.B. / Bullough, P.A. / Tzokov, S.B. / Agirre, J. / Li, F.L. / Rice, D.W.
History
DepositionMar 25, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alginate lyase
B: Alginate lyase
C: Alginate lyase
D: Alginate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)354,54031
Polymers353,0714
Non-polymers1,46927
Water14,988832
1
A: Alginate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,99213
Polymers88,2681
Non-polymers72512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alginate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,73110
Polymers88,2681
Non-polymers4649
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Alginate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,5487
Polymers88,2681
Non-polymers2816
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Alginate lyase


Theoretical massNumber of molelcules
Total (without water)88,2681
Polymers88,2681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)261.324, 394.812, 112.187
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1176-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Alginate lyase


Mass: 88267.664 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Defluviitalea phaphyphila (bacteria) / References: UniProt: A0A4Y5UXE1*PLUS

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Non-polymers , 7 types, 859 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 832 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 4.09 Å3/Da / Density % sol: 69.93 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 6.5 / Details: 15% PEG 6000, 0.1 M magnesium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97179 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Apr 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97179 Å / Relative weight: 1
ReflectionResolution: 2.069→98.898 Å / Num. obs: 348350 / % possible obs: 99.5 % / Redundancy: 7.3 % / Biso Wilson estimate: 32.327 Å2 / CC1/2: 0.992 / Net I/σ(I): 11
Reflection shellResolution: 2.069→2.11 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 16738 / CC1/2: 0.541

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
Aimlessdata reduction
pointlessdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.069→98.898 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.918 / WRfactor Rfree: 0.219 / WRfactor Rwork: 0.203 / SU B: 9.46 / SU ML: 0.123 / Average fsc free: 0.8638 / Average fsc work: 0.8715 / Cross valid method: FREE R-VALUE / ESU R: 0.144 / ESU R Free: 0.133
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2402 17175 4.931 %
Rwork0.2221 331147 -
all0.223 --
obs-348322 99.458 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 45.922 Å2
Baniso -1Baniso -2Baniso -3
1--1.517 Å20 Å20 Å2
2---0.122 Å20 Å2
3---1.639 Å2
Refinement stepCycle: LAST / Resolution: 2.069→98.898 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21800 0 73 832 22705
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01322364
X-RAY DIFFRACTIONr_bond_other_d0.0020.01818027
X-RAY DIFFRACTIONr_angle_refined_deg1.5151.63830067
X-RAY DIFFRACTIONr_angle_other_deg1.3871.58141522
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1953076
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.89223.911128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.36153018
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.261578
X-RAY DIFFRACTIONr_chiral_restr0.0740.22442
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0227288
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024946
X-RAY DIFFRACTIONr_nbd_refined0.1950.24283
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1810.216191
X-RAY DIFFRACTIONr_nbtor_refined0.1640.211125
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.29017
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.21003
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0910.24
X-RAY DIFFRACTIONr_metal_ion_refined0.1870.217
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.180.223
X-RAY DIFFRACTIONr_nbd_other0.2320.259
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.250.212
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1530.22
X-RAY DIFFRACTIONr_mcbond_it3.5572.25312321
X-RAY DIFFRACTIONr_mcbond_other3.5572.25312320
X-RAY DIFFRACTIONr_mcangle_it4.6773.36515388
X-RAY DIFFRACTIONr_mcangle_other4.6773.36515389
X-RAY DIFFRACTIONr_scbond_it5.192.29810043
X-RAY DIFFRACTIONr_scbond_other5.192.29810044
X-RAY DIFFRACTIONr_scangle_it6.4813.31814679
X-RAY DIFFRACTIONr_scangle_other6.4813.31814680
X-RAY DIFFRACTIONr_lrange_it7.9125.9325052
X-RAY DIFFRACTIONr_lrange_other7.9125.92925050
X-RAY DIFFRACTIONr_ncsr_local_group_10.0430.0527629
X-RAY DIFFRACTIONr_ncsr_local_group_20.040.0527673
X-RAY DIFFRACTIONr_ncsr_local_group_30.040.059732
X-RAY DIFFRACTIONr_ncsr_local_group_40.040.0527603
X-RAY DIFFRACTIONr_ncsr_local_group_50.0390.059738
X-RAY DIFFRACTIONr_ncsr_local_group_60.0380.059733
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.069-2.1230.35711870.34823739X-RAY DIFFRACTION96.7887
2.123-2.1810.34212780.3223600X-RAY DIFFRACTION99.1827
2.181-2.2450.30512050.29323059X-RAY DIFFRACTION99.463
2.245-2.3140.29511440.27222408X-RAY DIFFRACTION99.4343
2.314-2.3890.27511510.25521755X-RAY DIFFRACTION99.5956
2.389-2.4730.25810380.24221101X-RAY DIFFRACTION99.5906
2.473-2.5670.26110270.22820378X-RAY DIFFRACTION99.6555
2.567-2.6710.23710050.21219656X-RAY DIFFRACTION99.749
2.671-2.790.239590.20618812X-RAY DIFFRACTION99.783
2.79-2.9260.2269300.20417991X-RAY DIFFRACTION99.8575
2.926-3.0850.2329310.20517139X-RAY DIFFRACTION99.8618
3.085-3.2720.2358720.22316201X-RAY DIFFRACTION99.7429
3.272-3.4980.2527870.23215322X-RAY DIFFRACTION99.8327
3.498-3.7780.2397640.22614229X-RAY DIFFRACTION100
3.778-4.1380.2167100.20413156X-RAY DIFFRACTION99.9928
4.138-4.6260.1865890.17411966X-RAY DIFFRACTION99.992
4.626-5.3420.2035250.18210631X-RAY DIFFRACTION100
5.342-6.5410.2414820.2228967X-RAY DIFFRACTION100
6.541-9.2470.1873810.1837017X-RAY DIFFRACTION99.9865
9.247-120.2652100.2274020X-RAY DIFFRACTION99.7406
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)
10.86490.2311-0.09160.6372-0.44330.8827-0.0051-0.06540.0996-0.01880.03660.0623-0.0634-0.0889-0.03150.01620.0296-0.01560.1853-0.0260.0668-24.9445116.7892-16.41
22.138-0.5460.12040.7326-0.02350.46460.06940.1987-0.3604-0.0025-0.03750.15210.0554-0.0179-0.0320.0429-0.0597-0.02020.3098-0.12080.1874-31.794993.7211-67.0071
31.28440.23380.00170.8206-0.17630.4546-0.07780.06970.0524-0.03450.15160.20540.0345-0.1866-0.07380.2867-0.00790.00830.32650.26780.5211-74.4405165.7516-44.9573
40.2415-0.31440.24091.1615-0.17850.4779-0.0808-0.11810.19310.13420.10970.0512-0.3129-0.1336-0.02890.67130.0140.02270.72890.03670.7946-72.7475156.31464.613
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 770
2X-RAY DIFFRACTION2B1 - 770
3X-RAY DIFFRACTION3C1 - 770
4X-RAY DIFFRACTION4D1 - 770

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