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- PDB-1o4y: THE THREE-DIMENSIONAL STRUCTURE OF BETA-AGARASE A FROM ZOBELLIA G... -

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Basic information

Entry
Database: PDB / ID: 1o4y
TitleTHE THREE-DIMENSIONAL STRUCTURE OF BETA-AGARASE A FROM ZOBELLIA GALACTANIVORANS
Componentsbeta-agarase A
KeywordsHYDROLASE / BETA-AGARASE / GLYCOSIDE HYDROLASE FAMILY 16 / AGAROSE DEGRADATION / CLEAVAGE OF BETA-1 / 4-D-GALACTOSE LINKAGES
Function / homology
Function and homology information


beta-agarase / beta-agarase activity / carbohydrate metabolic process / extracellular region
Similarity search - Function
: / Beta-agarase/YXIM esterase-like, galactose-binding domain-like / Beta-agarase / Secretion system C-terminal sorting domain / Secretion system C-terminal sorting domain / Glycosyl hydrolases family 16 / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / Jelly Rolls - #200 / Galactose-binding-like domain superfamily ...: / Beta-agarase/YXIM esterase-like, galactose-binding domain-like / Beta-agarase / Secretion system C-terminal sorting domain / Secretion system C-terminal sorting 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
Beta-agarase A / Beta-agarase A
Similarity search - Component
Biological speciesZobellia galactanivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.48 Å
AuthorsAllouch, J. / Jam, M. / Helbert, W. / Barbeyron, T. / Kloareg, B. / Henrissat, B. / Czjzek, M.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: The Three-dimensional Structures of Two {beta}-Agarases.
Authors: Allouch, J. / Jam, M. / Helbert, W. / Barbeyron, T. / Kloareg, B. / Henrissat, B. / Czjzek, M.
History
DepositionJul 29, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_conn.ptnr2_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
Remark 999sequence the author maintains that the sequence in the sequence database is incorrect

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: beta-agarase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0156
Polymers32,6641
Non-polymers3515
Water6,395355
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.314, 57.487, 89.054
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 beta-agarase A


Mass: 32663.861 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zobellia galactanivorans (bacteria) / Strain: DSIJ / Plasmid: PET20B / Production host: Escherichia coli (E. coli)
References: UniProt: Q9RGX9, UniProt: G0L322*PLUS, beta-agarase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / 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: 1.97 Å3/Da / Density % sol: 37 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 4.6
Details: 28% PEG 8000, 200 mM Ammonium sulphate, 100 mM Sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Temperature: 20.5 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
12.5 mg/mlprotein1drop
250 %(w/v)Tris1droppH7.5
325 mM1dropNaCl
428 %PEG80001reservoir
5200 mMammonium sulfate1reservoir
6100 mMsodium acetate1reservoirpH4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.38482, 1.38561
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 3, 2002
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.384821
21.385611
ReflectionResolution: 1.48→34 Å / Num. all: 43809 / Num. obs: 43809 / % possible obs: 99.5 % / Redundancy: 4 % / Rsym value: 0.039 / Net I/σ(I): 15.6
Reflection
*PLUS
Lowest resolution: 14.8 Å / Num. obs: 42255 / % possible obs: 99.7 % / Redundancy: 3.9 % / Num. measured all: 454198 / Rmerge(I) obs: 0.083
Reflection shell
*PLUS
% possible obs: 99.7 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
REFMACrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.48→34 Å / SU B: 1.041 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.064 / ESU R Free: 0.066
RfactorNum. reflection% reflection
Rfree0.176 2191 5 %
Rwork0.148 --
obs0.149 41392 99.49 %
Displacement parametersBiso mean: 10.97 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20 Å20 Å2
2---0.21 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.48→34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2203 0 22 355 2580
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.015
X-RAY DIFFRACTIONp_angle_d1.604
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord0.25
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
LS refinement shellResolution: 1.48→1.518 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.237 147
Rwork0.204 3011
Refinement
*PLUS
Lowest resolution: 14.8 Å / % reflection Rfree: 5 % / Rfactor Rwork: 0.149
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.6

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