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- PDB-6xj9: Structure of PfGH50B -

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Basic information

Entry
Database: PDB / ID: 6xj9
TitleStructure of PfGH50B
ComponentsAgarase
KeywordsHYDROLASE / Glycoside hydrolase
Function / homologyAgarase, CBM-like domain / Agarase CBM like domain / Glycoside hydrolase, family 42, N-terminal / Beta-galactosidase / beta-galactosidase complex / beta-galactosidase activity / Glycoside hydrolase superfamily / carbohydrate metabolic process / Agarase
Function and homology information
Biological speciesPseudoalteromonas fuliginea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsPluvinage, B. / Boraston, A.B.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2020
Title: The structure of PfGH50B, an agarase from the marine bacterium Pseudoalteromonas fuliginea PS47
Authors: Pluvinage, B. / Robb, C.S. / Jeffries, R. / Boraston, A.B.
History
DepositionJun 23, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Agarase
B: Agarase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,1774
Polymers173,0532
Non-polymers1242
Water6,521362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint2 kcal/mol
Surface area54170 Å2
Unit cell
Length a, b, c (Å)73.240, 76.260, 269.860
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Agarase


Mass: 86526.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudoalteromonas fuliginea (bacteria) / Gene: EUZ79_06745 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A5B0UCF9
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / Source method: isolated from a natural source / Formula: H2O
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: 2.18 Å3/Da / Density % sol: 43.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 20% PEG 3350, 0.2M CaCl2, 0.1M MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.97932 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: May 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 2→29.98 Å / Num. obs: 99945 / % possible obs: 97.1 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rrim(I) all: 0.068 / Net I/σ(I): 18.3
Reflection shellResolution: 2→2.03 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 3724 / CC1/2: 0.723 / Rrim(I) all: 0.647 / % possible all: 74.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0258refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BQ2

4bq2


Resolution: 2→29.67 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.906 / SU B: 5.47 / SU ML: 0.151 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.222 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2692 5132 5.1 %RANDOM
Rwork0.2244 ---
obs0.2267 94757 96.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 87.79 Å2 / Biso mean: 36.903 Å2 / Biso min: 13.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å20 Å2
2--0.05 Å20 Å2
3----0.48 Å2
Refinement stepCycle: final / Resolution: 2→29.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10969 0 8 362 11339
Biso mean--52.75 30.42 -
Num. residues----1387
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01211338
X-RAY DIFFRACTIONr_angle_refined_deg0.9941.6315405
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.68951394
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.29823.24608
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.433151772
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.631549
X-RAY DIFFRACTIONr_chiral_restr0.0810.21447
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028904
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 271 -
Rwork0.295 5380 -
all-5651 -
obs--75.21 %

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