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- PDB-6jow: Exo-beta-D-glucosaminidase from Pyrococcus furiosus -

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Basic information

Entry
Database: PDB / ID: 6jow
TitleExo-beta-D-glucosaminidase from Pyrococcus furiosus
ComponentsBeta-galactosidase
KeywordsHYDROLASE / Glycoside hydrolase family 35
Function / homology
Function and homology information


beta-galactosidase complex / beta-galactosidase activity / carbohydrate metabolic process / metal ion binding
Similarity search - Function
: / GLMA-like, C-terminal / GLMA-like, glycosyl hydrolase domain / Beta-galactosidase trimerisation / Beta-galactosidase trimerisation domain / Glycoside hydrolase, family 42, N-terminal / Beta-galactosidase / Glycoside hydrolase, family 35 / Class I glutamine amidotransferase-like / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsMine, S. / Watanabe, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science25450143 Japan
CitationJournal: To Be Published
Title: Exo-beta-D-glucosaminidase from Pyrococcus furiosus
Authors: Mine, S. / Watanabe, M.
History
DepositionMar 24, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq
Item: _entity.pdbx_description / _entity_src_gen.gene_src_strain ..._entity.pdbx_description / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession
Revision 1.2Nov 22, 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
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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-galactosidase
B: Beta-galactosidase
C: Beta-galactosidase
D: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)357,74114
Polymers356,7164
Non-polymers1,02610
Water35,2371956
1
A: Beta-galactosidase
B: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,8717
Polymers178,3582
Non-polymers5135
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7460 Å2
ΔGint-60 kcal/mol
Surface area49930 Å2
MethodPISA
2
C: Beta-galactosidase
D: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,8717
Polymers178,3582
Non-polymers5135
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6880 Å2
ΔGint-43 kcal/mol
Surface area49960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.130, 149.597, 147.315
Angle α, β, γ (deg.)90.00, 102.07, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Beta-galactosidase / Exo-beta-D-glucosaminidase


Mass: 89178.977 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: PF0363 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U3U2
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1956 / 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: 2.57 Å3/Da / Density % sol: 52.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% MPD, 100 mM Tris pH 8.5, 500 mM Sodium chloride, 8% PEG 8000

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Data collection

DiffractionMean temperature: 173 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Apr 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 356244 / % possible obs: 98.4 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.038 / Rrim(I) all: 0.1 / Χ2: 2.36 / Net I/σ(I): 10.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.75-1.783.20.444173440.170.270.5230.80996
1.78-1.813.30.431174200.2380.2570.5050.84396.3
1.81-1.853.50.419173740.3030.2450.4880.87796.6
1.85-1.893.60.398174550.4380.2240.460.94896.7
1.89-1.933.80.371176300.5290.2030.4261.00997.5
1.93-1.974.10.344176490.6770.1820.3921.0997.8
1.97-2.024.30.315177230.7750.1620.3561.15998.1
2.02-2.074.50.283178030.850.1410.3181.24498.5
2.07-2.144.70.255178070.8980.1240.2851.34498.7
2.14-2.24.90.228178560.9330.1080.2531.44498.6
2.2-2.285.20.206178380.9540.0940.2271.66698.8
2.28-2.385.30.182178990.9680.0810.21.77699
2.38-2.485.60.158178810.9780.0690.1731.82599
2.48-2.615.80.135179550.9850.0580.1481.93199.2
2.61-2.786.10.113180070.9910.0470.1222.1199.4
2.78-2.996.30.101180060.9930.0410.1092.59199.5
2.99-3.296.70.093180900.9940.0370.13.72999.6
3.29-3.777.10.073180770.9960.0280.0794.03399.7
3.77-4.757.40.064181270.9960.0250.0694.46599.5
4.75-507.70.062183030.9960.0230.0664.49399.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
PHENIXmodel building
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GSM

5gsm


Resolution: 1.75→30 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.955 / SU B: 9.424 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21995 17963 5 %RANDOM
Rwork0.14797 ---
obs0.15161 338231 98.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.453 Å2
Baniso -1Baniso -2Baniso -3
1-2.36 Å20 Å22.73 Å2
2---4.45 Å20 Å2
3---0.85 Å2
Refinement stepCycle: 1 / Resolution: 1.75→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25252 0 66 1956 27274
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01326105
X-RAY DIFFRACTIONr_bond_other_d0.0170.01724160
X-RAY DIFFRACTIONr_angle_refined_deg1.8621.64435467
X-RAY DIFFRACTIONr_angle_other_deg1.661.57155988
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.51153060
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.1322.3211435
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.072154492
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.09515153
X-RAY DIFFRACTIONr_chiral_restr0.0930.23220
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0228858
X-RAY DIFFRACTIONr_gen_planes_other0.0080.025750
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_it5.7583.37912216
X-RAY DIFFRACTIONr_mcbond_other5.7553.37812215
X-RAY DIFFRACTIONr_mcangle_it6.8045.07315272
X-RAY DIFFRACTIONr_mcangle_other6.8045.07315273
X-RAY DIFFRACTIONr_scbond_it7.1133.76913889
X-RAY DIFFRACTIONr_scbond_other7.1133.76913890
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.15.47420192
X-RAY DIFFRACTIONr_long_range_B_refined8.44939.53830935
X-RAY DIFFRACTIONr_long_range_B_other8.39139.21530468
X-RAY DIFFRACTIONr_rigid_bond_restr14.128350265
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.747→1.793 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 1223 -
Rwork0.335 23281 -
obs--91.66 %

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