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- PDB-3f95: Crystal Structure of Extra C-terminal Domain (X) of Exo-1,3/1,4-b... -

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Basic information

Entry
Database: PDB / ID: 3f95
TitleCrystal Structure of Extra C-terminal Domain (X) of Exo-1,3/1,4-beta-glucanase (ExoP) from Pseudoalteromonas sp. BB1
ComponentsBeta-glucosidase
KeywordsHYDROLASE / beta-sandwich
Function / homology
Function and homology information


glucan catabolic process / beta-glucosidase / beta-glucosidase activity / metal ion binding
Similarity search - Function
ExoP, galactose-binding-like domain / Galactose-binding domain-like / Galactose-binding lectin / 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 ...ExoP, galactose-binding-like domain / Galactose-binding domain-like / Galactose-binding lectin / 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 / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesPseudoalteromonas sp. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 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 13, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Dec 21, 2011Group: Database references
Revision 1.3Dec 27, 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 / struct_ncs_dom_lim / 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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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: Beta-glucosidase
B: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8297
Polymers42,6522
Non-polymers1775
Water7,764431
1
A: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3973
Polymers21,3261
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4324
Polymers21,3261
Non-polymers1063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.416, 87.882, 56.459
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 4

Dom-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1AA632 - 8134 - 185
2BB634 - 8136 - 185

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Components

#1: Protein Beta-glucosidase


Mass: 21325.889 Da / Num. of mol.: 2 / Fragment: UNP residues 657-840
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
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 431 / 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: 2.14 Å3/Da / Density % sol: 42.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES-NaOH, pH6.5, 25% PEG6000, 0.2M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K

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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: Jul 13, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→21.75 Å / Num. all: 34511 / Num. obs: 34484 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 21.257 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 18.5
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.279 / Mean I/σ(I) obs: 3.8 / Num. unique all: 4916 / % possible all: 99.2

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→21.75 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.524 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.136 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23391 1737 5 %RANDOM
Rwork0.1883 ---
all0.19055 32837 --
obs0.19055 32712 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.025 Å2
Baniso -1Baniso -2Baniso -3
1-1.13 Å20 Å20 Å2
2---0.33 Å20 Å2
3----0.8 Å2
Refinement stepCycle: LAST / Resolution: 1.8→21.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2641 0 5 431 3077
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222764
X-RAY DIFFRACTIONr_angle_refined_deg1.6351.9693760
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1135366
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.4625.315111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.77915495
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1561512
X-RAY DIFFRACTIONr_chiral_restr0.1190.2437
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022042
X-RAY DIFFRACTIONr_nbd_refined0.2030.21198
X-RAY DIFFRACTIONr_nbtor_refined0.2970.21889
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2334
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2350.270
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2250.231
X-RAY DIFFRACTIONr_mcbond_it0.9731.51846
X-RAY DIFFRACTIONr_mcangle_it1.61822852
X-RAY DIFFRACTIONr_scbond_it2.28931063
X-RAY DIFFRACTIONr_scangle_it3.514.5899
Refine LS restraints NCS

Auth asym-ID: A / Ens-ID: 1 / Number: 1297 / Refine-ID: X-RAY DIFFRACTION

Dom-IDTypeRms dev position (Å)Weight position
1medium positional0.380.5
2medium thermal1.052
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 134 -
Rwork0.241 2367 -
obs--98.78 %

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