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- PDB-3rrx: Crystal Structure of Q683A mutant of Exo-1,3/1,4-beta-glucanase (... -

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Basic information

Entry
Database: PDB / ID: 3rrx
TitleCrystal Structure of Q683A mutant of Exo-1,3/1,4-beta-glucanase (ExoP) from Pseudoalteromonas sp. BB1
ComponentsExo-1,3/1,4-beta-glucanase
KeywordsHYDROLASE / (ALPHA/BETA)8 BARREL / (ALPHA/BETA)6 SHEET
Function / homology
Function and homology information


beta-glucosidase / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / metal ion binding
Similarity search - Function
ExoP, galactose-binding-like domain / Galactose-binding domain-like / Glycoside hydrolase family 3 C-terminal domain / Glycoside hydrolase, family 3, N-terminal domain / Glycoside hydrolase family 3 C-terminal domain / Glycosyl hydrolase family 3 C-terminal domain / Glycoside hydrolase family 3 C-terminal domain superfamily / Glycoside hydrolase, family 3, N-terminal / Glycoside hydrolase, family 3, N-terminal domain superfamily / Glycosyl hydrolase family 3 N terminal domain ...ExoP, galactose-binding-like domain / Galactose-binding domain-like / Glycoside hydrolase family 3 C-terminal domain / Glycoside hydrolase, family 3, N-terminal domain / Glycoside hydrolase family 3 C-terminal domain / Glycosyl hydrolase family 3 C-terminal domain / Glycoside hydrolase family 3 C-terminal domain superfamily / Glycoside hydrolase, family 3, N-terminal / Glycoside hydrolase, family 3, N-terminal domain superfamily / Glycosyl hydrolase family 3 N terminal domain / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPseudoalteromonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsNakatani, Y. / Cutfield, S.M. / Cutfield, J.F.
Citation
Journal: Febs J. / Year: 2012
Title: Structure and activity of exo-1,3/1,4-beta-glucanase from marine bacterium Pseudoalteromonas sp. BB1 showing a novel C-terminal domain
Authors: Nakatani, Y. / Cutfield, S.M. / Cowieson, N.P. / Cutfield, J.F.
#1: Journal: Appl.Environ.Microbiol. / Year: 2010
Title: Discovery and characterization of a distinctive exo-1,3/1,4-{beta}-glucanase from the marine bacterium Pseudoalteromonas sp. strain BB1
Authors: Nakatani, Y. / Lamont, I.L. / Cutfield, J.F.
History
DepositionMay 1, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Nov 1, 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_ref_seq_dif / 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_asym_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_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_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_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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Exo-1,3/1,4-beta-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,7525
Polymers90,5651
Non-polymers1874
Water11,061614
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.247, 178.601, 176.047
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1169-

HOH

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Components

#1: Protein Exo-1,3/1,4-beta-glucanase


Mass: 90564.523 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 28-840 / Mutation: Q683A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudoalteromonas sp. (bacteria) / Strain: BB1 / Gene: exoP / Plasmid: PET21(D) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS
References: UniProt: Q0QJA3, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 614 / Source method: isolated from a natural source / Formula: H2O

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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: 2.96 Å3/Da / Density % sol: 58.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Bis-Tris propane pH 6.5, 20% PEG 3350, 0.2M sodium sulphate, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 16, 2010
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.9→19.98 Å / Num. obs: 84347 / % possible obs: 99.4 % / Redundancy: 4.3 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 15.2
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3 / Num. unique all: 12277 / Rsym value: 0.45 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3USZ

3usz


Resolution: 1.9→19.98 Å / FOM work R set: 0.8892 / SU ML: 0.18 / σ(F): 1.34 / Phase error: 18.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1897 4214 5 %RANDOM
Rwork0.1624 ---
obs0.1638 84270 99.36 %-
all-88484 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.32 Å2 / ksol: 0.411 e/Å3
Displacement parametersBiso mean: 19.987 Å2
Baniso -1Baniso -2Baniso -3
1-17.9666 Å2-0 Å20 Å2
2---1.5279 Å2-0 Å2
3---2.4551 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4823 0 10 614 5447
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074966
X-RAY DIFFRACTIONf_angle_d16740
X-RAY DIFFRACTIONf_dihedral_angle_d12.2551791
X-RAY DIFFRACTIONf_chiral_restr0.075733
X-RAY DIFFRACTIONf_plane_restr0.004879
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9-1.96790.26644280.24317942100
1.9679-2.04660.23563920.20497982100
2.0466-2.13960.20754280.18417989100
2.1396-2.25230.20034200.16877972100
2.2523-2.39320.20854210.16588023100
2.3932-2.57760.19453940.1628005100
2.5776-2.83630.18114250.16198042100
2.8363-3.24520.19924460.1565799899
3.2452-4.08290.15714070.1352800698
4.0829-19.98180.1774530.1574809797

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