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- PDB-4q8l: Crystal structure of polysacchride lyase family 18 aly-SJ02 r-CATD -

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Basic information

Entry
Database: PDB / ID: 4q8l
TitleCrystal structure of polysacchride lyase family 18 aly-SJ02 r-CATD
ComponentsAlginase
KeywordsLYASE / Alginate lyase
Function / homology
Function and homology information


hydrolase activity, acting on glycosyl bonds / metal ion binding
Similarity search - Function
Alginate lyase 2 / Alginate lyase / Carbohydrate-binding, CenC-like / Carbohydrate binding domain / Jelly Rolls - #200 / Galactose-binding-like domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesPseudoalteromonas (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.099 Å
AuthorsDong, S. / Li, C.Y. / Zhang, Y.Z.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Molecular insight into the role of the N-terminal extension in the maturation, substrate recognition, and catalysis of a bacterial alginate lyase from polysaccharide lyase family 18.
Authors: Dong, S. / Wei, T.D. / Chen, X.L. / Li, C.Y. / Wang, P. / Xie, B.B. / Qin, Q.L. / Zhang, X.Y. / Pang, X.H. / Zhou, B.C. / Zhang, Y.Z.
History
DepositionApr 28, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2015Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alginase
B: Alginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0724
Polymers49,9922
Non-polymers802
Water5,459303
1
A: Alginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0362
Polymers24,9961
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Alginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0362
Polymers24,9961
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.738, 66.738, 419.881
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Alginase


Mass: 24996.166 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudoalteromonas (bacteria) / Strain: SM0524 / Production host: Escherichia coli (E. coli) / References: UniProt: B2LME8*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 303 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsA SEQUENCE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST.

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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: 2.7 Å3/Da / Density % sol: 54.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 100mM phosphate-citrate (pH 4.2), 40% (w/v) PEG 300, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 10, 2013
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.099→50 Å / Num. all: 34080 / Num. obs: 34080 / % possible obs: 99.7 %
Reflection shellResolution: 2.1→2.18 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MLPHAREphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1J1T

1j1t


Resolution: 2.099→36.302 Å / SU ML: 0.2 / σ(F): 0 / Phase error: 18.53 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2213 1718 5.07 %RANDOM
Rwork0.1827 ---
obs0.1847 33912 99.69 %-
all-34080 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.082 Å2 / ksol: 0.387 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.8332 Å2-0 Å2-0 Å2
2--3.8332 Å20 Å2
3----7.6664 Å2
Refinement stepCycle: LAST / Resolution: 2.099→36.302 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3514 0 2 303 3819
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073584
X-RAY DIFFRACTIONf_angle_d1.0164861
X-RAY DIFFRACTIONf_dihedral_angle_d13.6911280
X-RAY DIFFRACTIONf_chiral_restr0.07541
X-RAY DIFFRACTIONf_plane_restr0.004649
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0988-2.16050.24451530.17612584100
2.1605-2.23020.23641600.16222600100
2.2302-2.30990.20391220.15652615100
2.3099-2.40240.20641430.15952615100
2.4024-2.51170.21311370.16922622100
2.5117-2.64410.24351330.17962662100
2.6441-2.80970.26981360.19282659100
2.8097-3.02650.2491630.1892663100
3.0265-3.33090.21321460.18832689100
3.3309-3.81250.2261330.1757270399
3.8125-4.80160.17391500.1668276399
4.8016-36.30780.23781420.22723019100

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