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- PDB-5gkq: Structure of PL6 family alginate lyase AlyGC mutant-R241A -

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Basic information

Entry
Database: PDB / ID: 5gkq
TitleStructure of PL6 family alginate lyase AlyGC mutant-R241A
ComponentsAlyGC mutant - R241A
KeywordsLYASE / Alginate lyase / PL6
Function / homologyPL-6 family / Chondroitinase B / Pectin lyase fold / Pectin lyase fold/virulence factor / metal ion binding / AlyGC mutant - R241A
Function and homology information
Biological speciesGlaciecola chathamensis S18K6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.565 Å
AuthorsZhang, Y.Z. / Wang, P. / Xu, F.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Novel Molecular Insights into the Catalytic Mechanism of Marine Bacterial Alginate Lyase AlyGC from Polysaccharide Lyase Family 6
Authors: Xu, F. / Dong, F. / Wang, P. / Cao, H.Y. / Li, C.Y. / Li, P.Y. / Pang, X.H. / Zhang, Y.Z. / Chen, X.L.
History
DepositionJul 5, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2017Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
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 / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AlyGC mutant - R241A
B: AlyGC mutant - R241A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,3815
Polymers160,5782
Non-polymers8033
Water5,459303
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-4 kcal/mol
Surface area51090 Å2
2
A: AlyGC mutant - R241A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,0523
Polymers80,2891
Non-polymers7632
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-9 kcal/mol
Surface area26600 Å2
MethodPISA
3
B: AlyGC mutant - R241A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,3292
Polymers80,2891
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-9 kcal/mol
Surface area26650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.658, 122.830, 195.332
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein AlyGC mutant - R241A


Mass: 80289.195 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glaciecola chathamensis S18K6 (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A1S4NYD8*PLUS
#2: Polysaccharide beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid- ...beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid


Type: oligosaccharide / Mass: 722.510 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpAb1-4DManpAb1-4DManpAb1-4DManpAb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a1122A-1b_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][b-D-ManpA]{[(4+1)][b-D-ManpA]{[(4+1)][b-D-ManpA]{[(4+1)][b-D-ManpA]{}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 303 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION. AUTHORS STATE THAT THE GENEBANK ACCESSION NUMBER IS WP_007984897.1 FOR THIS SEQUENCE.

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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: 3.09 Å3/Da / Density % sol: 60.16 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100mM HEPES-NaOH (pH 7.3), 8% ethylene glycol, 11% polyethylene glycol (PEG) 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9785 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.565→47.8 Å / Num. obs: 61999 / % possible obs: 96 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.141 / Net I/σ(I): 4.6
Reflection shellResolution: 2.565→2.657 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GKD
Resolution: 2.565→47.8 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2279 3009 4.86 %
Rwork0.1907 --
obs0.1926 61946 96.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.565→47.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11322 0 51 303 11676
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911592
X-RAY DIFFRACTIONf_angle_d1.03615725
X-RAY DIFFRACTIONf_dihedral_angle_d15.6866860
X-RAY DIFFRACTIONf_chiral_restr0.0681762
X-RAY DIFFRACTIONf_plane_restr0.0062088
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5646-2.60670.2904790.26251678X-RAY DIFFRACTION58
2.6067-2.65160.35471510.25872796X-RAY DIFFRACTION98
2.6516-2.69980.3381460.25132823X-RAY DIFFRACTION99
2.6998-2.75180.30961330.24522877X-RAY DIFFRACTION98
2.7518-2.80790.32951460.24112776X-RAY DIFFRACTION98
2.8079-2.8690.30561660.24222844X-RAY DIFFRACTION98
2.869-2.93570.26741490.23882809X-RAY DIFFRACTION98
2.9357-3.00910.29911530.22872845X-RAY DIFFRACTION98
3.0091-3.09050.31311420.24142831X-RAY DIFFRACTION98
3.0905-3.18140.27931350.22612819X-RAY DIFFRACTION97
3.1814-3.28410.27151510.2212781X-RAY DIFFRACTION96
3.2841-3.40140.25671520.21042836X-RAY DIFFRACTION98
3.4014-3.53760.23491240.19842872X-RAY DIFFRACTION98
3.5376-3.69850.20331410.19722861X-RAY DIFFRACTION98
3.6985-3.89340.21071340.18712879X-RAY DIFFRACTION98
3.8934-4.13720.23321210.16762895X-RAY DIFFRACTION98
4.1372-4.45650.18531480.14842879X-RAY DIFFRACTION98
4.4565-4.90460.14611540.12372865X-RAY DIFFRACTION97
4.9046-5.61340.16991680.15012915X-RAY DIFFRACTION99
5.6134-7.0690.21831570.19032993X-RAY DIFFRACTION100
7.069-49.30620.19611590.18823063X-RAY DIFFRACTION97

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