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- PDB-3usz: Crystal structure of truncated exo-1,3/1,4-beta-glucanase (EXOP) ... -

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Basic information

Entry
Database: PDB / ID: 3usz
TitleCrystal structure of truncated 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
: / beta-glucosidase
Similarity search - Component
Biological speciesPseudoalteromonas sp. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsNakatani, Y. / Cutfield, S.M. / Cutfield, J.F.
CitationJournal: Febs J. / Year: 2011
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.
History
DepositionNov 24, 2011Deposition site: RCSB / Processing site: PDBJ
SupersessionDec 21, 2011ID: 3F94
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 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_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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)90,9107
Polymers90,6221
Non-polymers2886
Water9,026501
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.054, 179.414, 177.177
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 90621.570 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 28-840
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

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Non-polymers , 5 types, 507 molecules

#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-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 501 / 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: 2.98 Å3/Da / Density % sol: 58.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M BIS TRIS PROPANE PH6.5, 20% PEG 3350, 0.2M K/NA TARTRATE, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 9, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→36.35 Å / Num. all: 62301 / Num. obs: 62062 / % possible obs: 97.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 26.4 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 11.7
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 1.9 / Num. unique all: 7986 / Rsym value: 0.446 / % possible all: 86.7

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EX1

1ex1


Resolution: 2.1→33.416 Å / Occupancy max: 1 / Occupancy min: 0.08 / FOM work R set: 0.8873 / SU ML: 0.52 / σ(F): 1.34 / Phase error: 18.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1936 3134 5.06 %RANDOM
Rwork0.1637 ---
obs0.1653 61947 97.32 %-
all-61953 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.648 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 75.53 Å2 / Biso mean: 27.2967 Å2 / Biso min: 11.88 Å2
Baniso -1Baniso -2Baniso -3
1-10.0371 Å2-0 Å2-0 Å2
2---5.7368 Å20 Å2
3----4.3002 Å2
Refinement stepCycle: LAST / Resolution: 2.1→33.416 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4832 0 15 501 5348
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095054
X-RAY DIFFRACTIONf_angle_d1.0686876
X-RAY DIFFRACTIONf_dihedral_angle_d12.9361835
X-RAY DIFFRACTIONf_chiral_restr0.077745
X-RAY DIFFRACTIONf_plane_restr0.003897
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1-2.13280.30481050.2719224581
2.1328-2.16780.26071310.2611232286
2.1678-2.20520.28681210.2514246191
2.2052-2.24530.2831220.221258795
2.2453-2.28840.25451580.2016267699
2.2884-2.33510.21951630.17832695100
2.3351-2.38590.2291480.18382692100
2.3859-2.44140.22571450.17742730100
2.4414-2.50240.20061310.1682719100
2.5024-2.57010.20991310.16682742100
2.5701-2.64570.22321490.15732716100
2.6457-2.7310.21471550.15852733100
2.731-2.82860.21011470.16962754100
2.8286-2.94180.19321330.15992721100
2.9418-3.07560.20031360.15692747100
3.0756-3.23760.16751530.15112738100
3.2376-3.44020.17331390.13912751100
3.4402-3.70550.15161510.1374273599
3.7055-4.07790.19661390.1516270998
4.0779-4.66660.15331510.1336271298
4.6666-5.87420.16421570.1396276299
5.8742-33.42050.17811690.1854286698

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