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- PDB-3ut0: Crystal structure of exo-1,3/1,4-beta-glucanase (EXOP) from Pseud... -

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Basic information

Entry
Database: PDB / ID: 3ut0
TitleCrystal structure 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 / BETA-SANDWICH
Function / homology
Function and homology information


glucan catabolic process / 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 / 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 ...ExoP, galactose-binding-like domain / Galactose-binding domain-like / Galactose-binding lectin / : / 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 / Jelly Rolls / TIM Barrel / Alpha-Beta Barrel / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Exo-1,3/1,4-beta-glucanase
Similarity search - Component
Biological speciesPseudoalteromonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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: 3F93
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_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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_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_asym_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_asym_id / _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_asym_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_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
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
B: Exo-1,3/1,4-beta-glucanase
C: Exo-1,3/1,4-beta-glucanase
D: Exo-1,3/1,4-beta-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)365,02639
Polymers362,4864
Non-polymers2,54035
Water14,916828
1
A: Exo-1,3/1,4-beta-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,35111
Polymers90,6221
Non-polymers73010
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Exo-1,3/1,4-beta-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,28910
Polymers90,6221
Non-polymers6689
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Exo-1,3/1,4-beta-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,28910
Polymers90,6221
Non-polymers6689
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Exo-1,3/1,4-beta-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,0978
Polymers90,6221
Non-polymers4757
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.908, 257.821, 85.605
Angle α, β, γ (deg.)90.00, 115.47, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNLEULEUchain 'A' and (resseq 5:63 or resseq 80:626 or resseq 634:769 )AA5 - 636 - 64
12THRTHRPROPROchain 'A' and (resseq 5:63 or resseq 80:626 or resseq 634:769 )AA80 - 62681 - 627
13SERSERASPASPchain 'A' and (resseq 5:63 or resseq 80:626 or resseq 634:769 )AA634 - 769635 - 770
21GLNGLNLEULEUchain 'B' and (resseq 5:63 or resseq 80:626 or resseq 634:769 )BB5 - 636 - 64
22THRTHRPROPROchain 'B' and (resseq 5:63 or resseq 80:626 or resseq 634:769 )BB80 - 62681 - 627
23SERSERASPASPchain 'B' and (resseq 5:63 or resseq 80:626 or resseq 634:769 )BB634 - 769635 - 770
31GLNGLNLEULEUchain 'C' and (resseq 5:63 or resseq 80:626 or resseq 634:769 )CC5 - 636 - 64
32THRTHRPROPROchain 'C' and (resseq 5:63 or resseq 80:626 or resseq 634:769 )CC80 - 62681 - 627
33SERSERASPASPchain 'C' and (resseq 5:63 or resseq 80:626 or resseq 634:769 )CC634 - 769635 - 770
41GLNGLNLEULEUchain 'D' and (resseq 5:63 or resseq 80:626 or resseq 634:769 )DD5 - 636 - 64
42THRTHRPROPROchain 'D' and (resseq 5:63 or resseq 80:626 or resseq 634:769 )DD80 - 62681 - 627
43SERSERASPASPchain 'D' and (resseq 5:63 or resseq 80:626 or resseq 634:769 )DD634 - 769635 - 770

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 90621.570 Da / Num. of mol.: 4 / 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, 863 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 828 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.33 Å3/Da / Density % sol: 47.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES-NAOH, PH7.5, 2% PEG 400, 2.0M AMMONIUM SULFATE, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 13, 2009
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. all: 144061 / Num. obs: 143421 / % possible obs: 97.9 % / Redundancy: 3.2 % / Biso Wilson estimate: 41.6 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 8
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 2.1 / Num. unique all: 20491 / Rsym value: 0.405 / % possible all: 95.9

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3USZ, 3F95

3usz

3f95


Resolution: 2.3→38.328 Å / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.746 / SU ML: 0.76 / σ(F): 1.33 / Phase error: 31.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2701 7201 5.03 %RANDOM
Rwork0.2227 ---
obs0.2252 143281 97.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.517 Å2 / ksol: 0.331 e/Å3
Displacement parametersBiso max: 109.47 Å2 / Biso min: 3.89 Å2
Baniso -1Baniso -2Baniso -3
1-3.8362 Å2-0 Å20.7984 Å2
2---9.3615 Å2-0 Å2
3---24.1857 Å2
Refinement stepCycle: LAST / Resolution: 2.3→38.328 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24780 0 134 828 25742
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00725468
X-RAY DIFFRACTIONf_angle_d1.03734563
X-RAY DIFFRACTIONf_dihedral_angle_d12.6719146
X-RAY DIFFRACTIONf_chiral_restr0.0713795
X-RAY DIFFRACTIONf_plane_restr0.0054460
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A5773X-RAY DIFFRACTIONPOSITIONAL0.052
12B5773X-RAY DIFFRACTIONPOSITIONAL0.052
13C5773X-RAY DIFFRACTIONPOSITIONAL0.057
14D5773X-RAY DIFFRACTIONPOSITIONAL0.056
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 (%)
2.3-2.38220.37597200.30931326996
2.3822-2.47760.35717000.28541334796
2.4776-2.59030.33166870.25941356597
2.5903-2.72680.34437090.26251349097
2.7268-2.89760.33457600.25631357198
2.8976-3.12120.3247280.25961367598
3.1212-3.43520.31646890.25311377499
3.4352-3.93180.25697440.21861357598
3.9318-4.9520.19937620.16621382299
4.952-38.33320.20797020.18761399299
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7339-0.1571-0.07050.7193-0.08030.52460.269-0.1622-0.60.43020.13870.63710.0015-0.29080.1665-0.3299-0.02930.1453-0.07730.0602-0.2305100.4332-8.137230.9391
20.53440.19250.12020.32730.00590.4630.01080.1220.1474-0.16070.03670.0712-0.1275-0.0330.04080.20220.03110.05660.02910.1295-0.0537110.104125.051911.0915
30.1739-0.00070.14360.15550.0040.12640.14961.0964-0.3372-0.62320.2056-0.585-0.04070.94790.2722-1.65640.63850.1364-1.4263-0.6034-1.002368.4127-14.8646-0.4648
40.2801-0.34330.1390.8365-0.28950.52150.0029-0.13220.14690.5175-0.0308-0.3032-0.24960.0720.00940.298-0.0927-0.03360.2044-0.03750.145467.126519.273919.2041
50.22570.10690.02450.41550.15090.055-0.1999-0.22450.23590.1771-0.12890.6206-0.2188-0.6282-0.3755-0.62590.0061-0.0313-1.2579-0.38090.205993.2094-62.65833.3778
60.44320.09370.10061.03390.1820.36120.072-0.1175-0.07310.3833-0.034-0.29880.21540.09310.04130.25470.03570.02660.09620.05290.1343117.4196-93.56866.0647
70.13910.07020.15390.61050.24590.1377-0.02120.69430.1307-0.98450.4351-0.3086-0.24671.13880.2604-0.5945-1.09860.1297-2.48320.0991-0.8414106.8005-56.127345.2101
80.105-0.0819-0.00120.8141-0.06480.2336-0.02540.1614-0.0339-0.61740.04040.2591-0.0266-0.0525-0.02180.5202-0.0929-0.1210.0627-0.05170.10990.53-91.948441.023
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and ((resseq 5:626))
2X-RAY DIFFRACTION2chain 'A' and ((resseq 632:816))
3X-RAY DIFFRACTION3chain 'B' and ((resseq 5:626))
4X-RAY DIFFRACTION4chain 'B' and ((resseq 634:814))
5X-RAY DIFFRACTION5chain 'C' and ((resseq 5:626))
6X-RAY DIFFRACTION6chain 'C' and ((resseq 634:814))
7X-RAY DIFFRACTION7chain 'D' and ((resseq 5:626))
8X-RAY DIFFRACTION8chain 'D' and ((resseq 634:815))

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