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

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Basic information

Entry
Database: PDB / ID: 3azy
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: 1.65 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)126,25920
Polymers124,9464
Non-polymers1,31316
Water14,574809
1
A: Laminarinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4694
Polymers31,2361
Non-polymers2323
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Laminarinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5655
Polymers31,2361
Non-polymers3284
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Laminarinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6616
Polymers31,2361
Non-polymers4245
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Laminarinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5655
Polymers31,2361
Non-polymers3284
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)120.420, 120.420, 107.195
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.: 12 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 809 / 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: 3.11 Å3/Da / Density % sol: 60.45 %
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: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 24, 2010
Details: Vertically Collimating Premirror, Toroidal Focusing Mirror
RadiationMonochromator: LN2-Cooled Fixed-Exit Double Crystal Si(111) Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→30 Å / Num. all: 183497 / Num. obs: 183216 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 5.6 % / Biso Wilson estimate: 33.4 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 26.8
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 3.2 / Num. unique all: 18166 / % 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 3AZX

3azx


Resolution: 1.65→24.6 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.929 / SU ML: 0.046 / Isotropic thermal model: Isotropic with TLS / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19226 9197 5 %RANDOM
Rwork0.16288 ---
obs0.16436 183046 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.41 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20 Å20 Å2
2--0.61 Å20 Å2
3----1.23 Å2
Refinement stepCycle: LAST / Resolution: 1.65→24.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8132 0 64 809 9005
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0228498
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4221.93111586
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.12151012
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.43224.889450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.667151274
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7471524
X-RAY DIFFRACTIONr_chiral_restr0.1040.21131
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216764
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_it1.2391.54977
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.04527995
X-RAY DIFFRACTIONr_scbond_it3.0933521
X-RAY DIFFRACTIONr_scangle_it4.5454.53588
X-RAY DIFFRACTIONr_rigid_bond_restr1.51538498
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.649→1.738 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.245 1338 -
Rwork0.194 25165 -
obs-26503 99.84 %
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)
11.70440.0088-0.09030.5760.01310.88080.1264-0.0904-0.10730.0062-0.05880.01140.05190.0228-0.06760.0296-0.0121-0.02460.01340.00730.0219-8.479936.674899.3787
20.844-0.37290.14181.4742-0.41310.9645-0.0859-0.17620.00880.18280.12340.0403-0.0457-0.0723-0.03750.07150.0392-0.00810.0519-0.01130.0147-29.074475.777188.3356
31.7137-0.25020.35390.653-0.06351.00810.11120.11230.0149-0.1165-0.11050.02690.0213-0.017-0.00070.02360.022-0.00440.03920.010.012915.819329.061770.8719
40.52060.0371-0.08261.47550.14070.79560.00050.03980.0173-0.02550.09970.0955-0.03490.0027-0.10020.0043-0.0006-0.00090.00980.00610.0273-21.94252.420459.6112
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 258
2X-RAY DIFFRACTION2B8 - 258
3X-RAY DIFFRACTION3C8 - 258
4X-RAY DIFFRACTION4D8 - 258

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