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- PDB-3wz1: Catalytic domain of beta-agarase from Microbulbifer thermotoleran... -

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Basic information

Entry
Database: PDB / ID: 3wz1
TitleCatalytic domain of beta-agarase from Microbulbifer thermotolerans JAMB-A94
ComponentsAgarase
KeywordsHYDROLASE / Glycoside hydrolase family 16 / Beta-jelly roll fold / Beta-agarase / Agarose
Function / homology
Function and homology information


beta-agarase activity / carbohydrate binding / carbohydrate metabolic process
Similarity search - Function
Beta-agarase / Cellulose binding, type IV / Cellulose Binding Domain Type IV / Carbohydrate binding module (family 6) / Glycosyl hydrolases family 16 / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Jelly Rolls - #200 ...Beta-agarase / Cellulose binding, type IV / Cellulose Binding Domain Type IV / Carbohydrate binding module (family 6) / Glycosyl hydrolases family 16 / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / 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 speciesMicrobulbifer thermotolerans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsTakagi, E. / Hatada, Y. / Akita, M. / Ohta, Y. / Yokoi, G. / Miyazaki, T. / Nishikawa, A. / Tonozuka, T.
CitationJournal: Biosci.Biotechnol.Biochem. / Year: 2015
Title: Crystal structure of the catalytic domain of a GH16 beta-agarase from a deep-sea bacterium, Microbulbifer thermotolerans JAMB-A94
Authors: Takagi, E. / Hatada, Y. / Akita, M. / Ohta, Y. / Yokoi, G. / Miyazaki, T. / Nishikawa, A. / Tonozuka, T.
History
DepositionSep 12, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Nov 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_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.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_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: Agarase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2575
Polymers32,0271
Non-polymers2304
Water4,684260
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.624, 69.394, 90.367
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Agarase / Beta-agarase


Mass: 32027.268 Da / Num. of mol.: 1 / Fragment: UNP residues 19-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Microbulbifer thermotolerans (bacteria)
Strain: JAMB-A94 / Gene: agaA / Plasmid: pEXBS / Production host: Bacillus subtilis (bacteria) / Strain (production host): ISW1214 / References: UniProt: Q6F4N4, beta-agarase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.43 Å3/Da / Density % sol: 49.36 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1M trisodium citrate, 0.3M ammonium nitrtate, 3% ethanol, 100mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: May 25, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 41972 / % possible obs: 100 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.031 / Net I/σ(I): 59.5
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.124 / Mean I/σ(I) obs: 18.3 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ATF

4atf


Resolution: 1.6→37.86 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.96 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16463 2117 5.1 %RANDOM
Rwork0.15191 ---
obs0.15256 39772 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.759 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.6→37.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2236 0 14 260 2510
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192355
X-RAY DIFFRACTIONr_bond_other_d00.022074
X-RAY DIFFRACTIONr_angle_refined_deg1.4621.9243223
X-RAY DIFFRACTIONr_angle_other_deg3.6334783
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6725283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.97623.417120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.2515337
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.231515
X-RAY DIFFRACTIONr_chiral_restr0.0840.2319
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212712
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02591
X-RAY DIFFRACTIONr_mcbond_it0.7221.1581115
X-RAY DIFFRACTIONr_mcbond_other0.7171.1571114
X-RAY DIFFRACTIONr_mcangle_it1.1911.7351394
X-RAY DIFFRACTIONr_mcangle_other1.191.7361395
X-RAY DIFFRACTIONr_scbond_it1.041.2431240
X-RAY DIFFRACTIONr_scbond_other1.0381.2431240
X-RAY DIFFRACTIONr_scangle_other1.61.8261826
X-RAY DIFFRACTIONr_long_range_B_refined3.68710.3612904
X-RAY DIFFRACTIONr_long_range_B_other3.3189.852787
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.158 149 -
Rwork0.155 2894 -
obs--99.64 %

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