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- PDB-5xnr: Truncated AlyQ with CBM32 and alginate lyase domains -

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Basic information

Entry
Database: PDB / ID: 5xnr
TitleTruncated AlyQ with CBM32 and alginate lyase domains
ComponentsAlyQ
KeywordsLYASE / Alginate lyase / CBM32
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Alginate lyase 2 / Alginate lyase / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Galactose-binding domain-like / Jelly Rolls - #200 / Galactose-binding-like domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls ...Alginate lyase 2 / Alginate lyase / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Galactose-binding domain-like / Jelly Rolls - #200 / Galactose-binding-like domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / : / PHOSPHATE ION / AlyQ
Similarity search - Component
Biological speciesPersicobacter sp. CCB-QB2 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsTeh, A.H. / Sim, P.F.
Funding support Malaysia, 1items
OrganizationGrant numberCountry
Malaysia
CitationJournal: Sci Rep / Year: 2017
Title: Functional and Structural Studies of a Multidomain Alginate Lyase from Persicobacter sp. CCB-QB2.
Authors: Sim, P.F. / Furusawa, G. / Teh, A.H.
History
DepositionMay 24, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 20, 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

Downloads & links

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Assembly

Deposited unit
A: AlyQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1975
Polymers43,9641
Non-polymers2334
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area360 Å2
ΔGint-4 kcal/mol
Surface area17380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.317, 74.317, 179.733
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein AlyQ


Mass: 43963.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Persicobacter sp. CCB-QB2 (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3B6UEP6*PLUS

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Non-polymers , 5 types, 44 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsSequence of the protein has been deposited to NCBI with accession number WP_053404615.

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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: 2.82 Å3/Da / Density % sol: 56.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 30% PEG 3350, 0.1M sodium acetate pH 4.0, 0.2M potassium phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→37.19 Å / Num. obs: 22663 / % possible obs: 97.5 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.096 / Rrim(I) all: 0.117 / Χ2: 0.99 / Net I/σ(I): 5.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRrim(I) allΧ2% possible all
2.3-2.382.910.3962.10.4831.2198.4
2.38-2.482.940.3872.10.471.1397.9
2.48-2.592.910.3372.50.4111.2198
2.59-2.732.960.2842.80.3451.1397.5
2.73-2.92.970.2153.50.2611.0397.3
2.9-3.122.940.1584.50.1920.9597.5
3.12-3.442.90.1056.40.1270.998.1
3.44-3.932.860.0769.10.0920.8498.6
3.93-4.952.820.05611.90.0670.7798.1
4.95-37.162.80.051130.0610.7294.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
PDB_EXTRACTdata extraction
MOLREPphasing
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UAI

1uai


Resolution: 2.3→37.19 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.922 / SU B: 9.508 / SU ML: 0.212 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.305 / ESU R Free: 0.244
RfactorNum. reflection% reflectionSelection details
Rfree0.2745 1144 5.1 %RANDOM
Rwork0.2264 ---
obs0.2289 21500 97.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 113.67 Å2 / Biso mean: 39.063 Å2 / Biso min: 23.44 Å2
Baniso -1Baniso -2Baniso -3
1-2.4 Å2-0 Å2-0 Å2
2--2.4 Å2-0 Å2
3----4.79 Å2
Refinement stepCycle: final / Resolution: 2.3→37.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2991 0 11 40 3042
Biso mean--44.63 31.92 -
Num. residues----385
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0153067
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172561
X-RAY DIFFRACTIONr_angle_refined_deg1.3371.7274168
X-RAY DIFFRACTIONr_angle_other_deg0.4681.725998
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4015383
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.05421.75120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.30615405
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0391511
X-RAY DIFFRACTIONr_chiral_restr0.0570.2403
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023539
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02605
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.438 82 -
Rwork0.322 1567 -
all-1649 -
obs--98.45 %

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