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- PDB-3b01: Crystal structure of the laminarinase catalytic domain from Therm... -

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Basic information

Entry
Database: PDB / ID: 3b01
TitleCrystal structure of the laminarinase catalytic domain from Thermotoga maritima MSB8
ComponentsLaminarinase
KeywordsHYDROLASE / beta-jelly roll fold / Glycosyl hydrolase family 16 / Laminarinase / Endo-1 / 3-beta-glucanase
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / metal ion binding
Similarity search - Function
: / Carbohydrate-binding, CenC-like / Carbohydrate binding domain / Glycosyl hydrolases family 16 / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / Jelly Rolls - #200 / Galactose-binding-like domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls ...: / Carbohydrate-binding, CenC-like / Carbohydrate binding domain / Glycosyl hydrolases family 16 / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / Jelly Rolls - #200 / Galactose-binding-like domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsJeng, W.Y. / Wang, N.C. / Wang, A.H.J.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Crystal structures of the laminarinase catalytic domain from Thermotoga maritima MSB8 in complex with inhibitors: essential residues for beta-1,3 and beta-1,4 glucan selection.
Authors: Jeng, W.Y. / Wang, N.C. / Lin, C.T. / Shyur, L.F. / Wang, A.H.
History
DepositionJun 3, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: 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_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_label_asym_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_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: Laminarinase
B: Laminarinase
C: Laminarinase
D: Laminarinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,98119
Polymers124,9464
Non-polymers1,03515
Water11,962664
1
A: Laminarinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3733
Polymers31,2361
Non-polymers1362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Laminarinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6006
Polymers31,2361
Non-polymers3645
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Laminarinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6006
Polymers31,2361
Non-polymers3645
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Laminarinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4084
Polymers31,2361
Non-polymers1723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)120.305, 120.305, 107.154
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein
Laminarinase


Mass: 31236.436 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 204-466
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8, ATCC43589 / Gene: TM_0024 / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 (DE3)
References: UniProt: Q9WXN1, glucan endo-1,3-beta-D-glucosidase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 664 / 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: 3.1 Å3/Da / Density % sol: 60.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 41-46% (w/v) polypropylenglycol P400, 0.05-0.2M (NH4)2SO4, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.97622 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 6, 2010 / Details: Vertically Focusing Mirror
RadiationMonochromator: Horizontally Focusing Single Crystal Si(111) Bent Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 1.87→30 Å / Num. all: 125924 / Num. obs: 125562 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 6.2 % / Biso Wilson estimate: 39 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 27.4
Reflection shellResolution: 1.87→1.94 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.517 / Mean I/σ(I) obs: 3.9 / Num. unique all: 12561 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3AZY

3azy


Resolution: 1.87→27.5 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.313 / SU ML: 0.059 / Isotropic thermal model: Isotropic with TLS / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18771 6298 5 %RANDOM
Rwork0.1517 ---
obs0.15348 125430 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.415 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å20 Å2
2--0.18 Å20 Å2
3----0.37 Å2
Refinement stepCycle: LAST / Resolution: 1.87→27.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8123 0 47 664 8834
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0228535
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4061.92911638
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.99451025
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.72924.889450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.658151279
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3391524
X-RAY DIFFRACTIONr_chiral_restr0.1010.21139
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216812
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3481.55023
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.28928067
X-RAY DIFFRACTIONr_scbond_it3.37833512
X-RAY DIFFRACTIONr_scangle_it5.1284.53567
X-RAY DIFFRACTIONr_rigid_bond_restr1.76838535
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.869→1.97 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.23 908 -
Rwork0.17 17334 -
obs-18242 99.85 %
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)
11.7260.0008-0.03730.40930.04260.67270.1318-0.0858-0.1014-0.0147-0.05580.01840.01380.0103-0.0760.0466-0.02-0.02750.01930.00830.0245-8.337836.60799.2795
20.5954-0.45670.14161.4732-0.38340.6608-0.1326-0.13050.0060.170.15330.0117-0.0473-0.049-0.02070.09890.0542-0.01360.0535-0.00810.0043-29.069475.828188.2792
31.7054-0.35120.34310.549-0.09360.76190.12390.10360.0153-0.0843-0.1211-0.00140.0108-0.0067-0.00290.02330.01790.00110.06060.01080.003415.84229.044570.8054
40.39670.0593-0.13181.39930.11410.55020.01390.01960.0054-0.01530.07570.1052-0.00880.0176-0.08960.0197-0.0019-0.01080.02260.00230.033-21.963752.396259.5774
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 258
2X-RAY DIFFRACTION2B9 - 258
3X-RAY DIFFRACTION3C8 - 258
4X-RAY DIFFRACTION4D8 - 258

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