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- PDB-1o4z: THE THREE-DIMENSIONAL STRUCTURE OF BETA-AGARASE B FROM ZOBELLIA G... -

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Basic information

Entry
Database: PDB / ID: 1o4z
TitleTHE THREE-DIMENSIONAL STRUCTURE OF BETA-AGARASE B FROM ZOBELLIA GALACTANIVORANS
Componentsbeta-agarase B
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 / cell outer membrane / carbohydrate metabolic process / protein homodimerization activity
Similarity search - Function
Beta-agarase / Glycosyl hydrolases family 16 / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / Jelly Rolls - #200 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesZobellia galactanivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: beta-agarase B
B: beta-agarase B
C: beta-agarase B
D: beta-agarase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,38917
Polymers160,2264
Non-polymers1,16313
Water15,997888
1
A: beta-agarase B
B: beta-agarase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,7069
Polymers80,1132
Non-polymers5937
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: beta-agarase B
D: beta-agarase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,6838
Polymers80,1132
Non-polymers5706
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.448, 105.350, 97.369
Angle α, β, γ (deg.)90.00, 94.13, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.9999, 0.0119, -0.00729), (-0.01221, 0.99897, -0.04378), (0.00677, 0.04386, 0.99901)40.619, 4.027, -48.259
2given(0.24143, 0.84866, 0.47062), (0.8613, -0.41083, 0.29898), (0.44707, 0.33316, -0.83014)-45.94651, -35.01696, 53.92286
3given(0.24246, 0.8772, 0.41442), (0.86057, -0.39168, 0.3256), (0.44793, 0.27769, -0.84985)-53.949, -18.072, 114.847

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Components

#1: Protein
beta-agarase B


Mass: 40056.523 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zobellia galactanivorans (bacteria) / Strain: DSIJ / Gene: agaB / Plasmid: PET20B / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RGX8, beta-agarase
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 888 / 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: 2.31 Å3/Da / Density % sol: 47 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: 58% methyl-pentane-diol 20 mM calcium chloride 100 mM Hepes , pH 7.5, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Temperature: 20.5 ℃ / 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
458 %MPD1reservoir
520 mM1reservoirCaCl2
6100 mMHEPES1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 1, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.3→95.35 Å / Num. all: 61473 / Num. obs: 61473 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rsym value: 0.106 / Net I/σ(I): 5.4
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.6 / Rsym value: 0.339 / % possible all: 99.8
Reflection
*PLUS
Lowest resolution: 24.8 Å / Num. obs: 64783 / Num. measured all: 428617 / Rmerge(I) obs: 0.106
Reflection shell
*PLUS
% possible obs: 99.9 % / Rmerge(I) obs: 0.339

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Processing

Software
NameVersionClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: BETA-AGARASE A

Resolution: 2.3→25 Å / SU B: 5.974 / SU ML: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.292 / ESU R Free: 0.218
RfactorNum. reflection% reflectionSelection details
Rfree0.22384 3282 5.1 %random
Rwork0.16567 ---
obs0.16862 61473 99.92 %-
all-61473 --
Displacement parametersBiso mean: 19.944 Å2
Baniso -1Baniso -2Baniso -3
1--0.51 Å20 Å20.29 Å2
2---0.83 Å20 Å2
3---1.3 Å2
Refinement stepCycle: LAST / Resolution: 2.3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9690 0 69 888 10647
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.011
X-RAY DIFFRACTIONp_angle_d1.33
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
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
Refinement
*PLUS
Lowest resolution: 24.8 Å / Rfactor Rfree: 0.224 / Rfactor Rwork: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.031
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.4

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