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- PDB-5gkd: Structure of PL6 family alginate lyase AlyGC -

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Basic information

Entry
Database: PDB / ID: 5gkd
TitleStructure of PL6 family alginate lyase AlyGC
ComponentsAlyGC
KeywordsLYASE / alginate lyase / PL6
Function / homologyPL-6 family / Chondroitinase B / Pectin lyase fold / Pectin lyase fold/virulence factor / metal ion binding / CARBONATE ION / PHOSPHATE ION / AlyGC
Function and homology information
Biological speciesGlaciecola chathamensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.194 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 4, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2017Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: AlyGC
B: AlyGC
C: AlyGC
D: AlyGC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)324,51540
Polymers321,5014
Non-polymers3,01436
Water44,9472495
1
A: AlyGC
D: AlyGC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,25720
Polymers160,7512
Non-polymers1,50718
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AlyGC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,12910
Polymers80,3751
Non-polymers7539
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: AlyGC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,12910
Polymers80,3751
Non-polymers7539
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.608, 142.840, 126.276
Angle α, β, γ (deg.)90.00, 111.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
AlyGC


Mass: 80375.312 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glaciecola chathamensis (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A1S4NYD7*PLUS

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Non-polymers , 5 types, 2531 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: PO4
#5: Chemical
ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CO3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2495 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.05 Å3/Da / Density % sol: 59.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 25% PEG1500, 100 mM SPG pH=8.5

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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: Jun 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.194→34.45 Å / Num. obs: 193472 / % possible obs: 98 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 5.9
Reflection shellResolution: 2.194→2.273 Å / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.194→34.45 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1973 9766 5.05 %
Rwork0.1653 --
obs0.1669 193435 98.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.194→34.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22668 0 176 2495 25339
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00823244
X-RAY DIFFRACTIONf_angle_d1.01531480
X-RAY DIFFRACTIONf_dihedral_angle_d14.80313768
X-RAY DIFFRACTIONf_chiral_restr0.0683484
X-RAY DIFFRACTIONf_plane_restr0.0054184
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1944-2.21940.26992890.21755242X-RAY DIFFRACTION85
2.2194-2.24550.24683130.20486152X-RAY DIFFRACTION100
2.2455-2.27290.24783050.20196193X-RAY DIFFRACTION100
2.2729-2.30160.26033320.20116233X-RAY DIFFRACTION99
2.3016-2.33190.2443620.1976155X-RAY DIFFRACTION99
2.3319-2.36380.23573250.18666093X-RAY DIFFRACTION99
2.3638-2.39760.24053160.18876149X-RAY DIFFRACTION99
2.3976-2.43340.22243540.18016122X-RAY DIFFRACTION99
2.4334-2.47140.23373560.18116152X-RAY DIFFRACTION99
2.4714-2.51190.23593270.18456163X-RAY DIFFRACTION99
2.5119-2.55520.24153300.18696096X-RAY DIFFRACTION99
2.5552-2.60170.25833120.18636163X-RAY DIFFRACTION99
2.6017-2.65170.24473220.18466129X-RAY DIFFRACTION99
2.6517-2.70580.23923430.18416103X-RAY DIFFRACTION98
2.7058-2.76460.22453310.18726061X-RAY DIFFRACTION98
2.7646-2.82890.23922890.18195945X-RAY DIFFRACTION96
2.8289-2.89960.21543010.1746198X-RAY DIFFRACTION99
2.8996-2.9780.22083410.1796206X-RAY DIFFRACTION100
2.978-3.06560.22723280.1836213X-RAY DIFFRACTION100
3.0656-3.16450.2093090.17886206X-RAY DIFFRACTION100
3.1645-3.27750.21743490.17536160X-RAY DIFFRACTION100
3.2775-3.40870.19383080.1726248X-RAY DIFFRACTION99
3.4087-3.56370.18373190.16066144X-RAY DIFFRACTION99
3.5637-3.75140.16663390.15256154X-RAY DIFFRACTION99
3.7514-3.98620.17553160.14616089X-RAY DIFFRACTION98
3.9862-4.29350.15073530.13946013X-RAY DIFFRACTION97
4.2935-4.72480.14273260.12276231X-RAY DIFFRACTION99
4.7248-5.40670.16342980.13196245X-RAY DIFFRACTION99
5.4067-6.8050.18013420.16216233X-RAY DIFFRACTION99
6.805-37.03550.15693310.15366178X-RAY DIFFRACTION97

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