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- PDB-1gon: b-glucosidase from Streptomyces sp -

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Basic information

Entry
Database: PDB / ID: 1gon
Titleb-glucosidase from Streptomyces sp
ComponentsBETA-GLUCOSIDASE
KeywordsHYDROLASE / GLYCOSYLTRANSFERASE / FAMILY 1 OF GLYCOSYL HYDROLASE
Function / homology
Function and homology information


beta-glucosidase / beta-glucosidase activity / cellulose catabolic process / cytosol
Similarity search - Function
Glycoside hydrolase, family 1, beta-glucosidase / Glycoside hydrolase family 1, active site / Glycosyl hydrolases family 1 active site. / Glycosyl hydrolases family 1, N-terminal conserved site / Glycosyl hydrolases family 1 N-terminal signature. / Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel ...Glycoside hydrolase, family 1, beta-glucosidase / Glycoside hydrolase family 1, active site / Glycosyl hydrolases family 1 active site. / Glycosyl hydrolases family 1, N-terminal conserved site / Glycosyl hydrolases family 1 N-terminal signature. / Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
: / Beta-glucosidase
Similarity search - Component
Biological speciesSTREPTOMYCES SP. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsGuasch, A. / Perez-Pons, J.A. / Vallmitjana, M. / Querol, E. / Coll, M.
Citation
Journal: To be Published
Title: Crystal Structure of a Family 1 Beta-Glucosidase from Streptomyces
Authors: Guasch, A. / Vallmitjana, M. / Perez, R. / Querol, E. / Perez-Pons, J.A. / Coll, M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Cloning, Overexpression, Crystallization and Preliminary X-Ray Analysis of a Family 1 Beta--Glucosidase from Streptomyces
Authors: Guash, A. / Vallmitjana, M. / Perez, R. / Querol, E. / Peez-Pons, J.A. / Coll, M.
History
DepositionOct 22, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 7, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BETA-GLUCOSIDASE
B: BETA-GLUCOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,25011
Polymers104,7582
Non-polymers1,4929
Water9,260514
1
A: BETA-GLUCOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0775
Polymers52,3791
Non-polymers6984
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: BETA-GLUCOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1736
Polymers52,3791
Non-polymers7945
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)96.312, 111.171, 185.246
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein BETA-GLUCOSIDASE


Mass: 52378.992 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES SP. (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q59976
#2: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Hg
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 514 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE PROTEIN WAS SUBMITED TO LIMITED PROTEOLYSIS WITH TRYPSIN. THE MAJOR TRYPSIN-CLEAVAGE SITES ...THE PROTEIN WAS SUBMITED TO LIMITED PROTEOLYSIS WITH TRYPSIN. THE MAJOR TRYPSIN-CLEAVAGE SITES CORRESPOND TO SER315 AND ARG 330.

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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: 2.48 Å3/Da / Density % sol: 48.03 %
Crystal growpH: 7.5 / Details: 1.9 M AMMONIUM SULFATE, 0.1 M HEPES PH 7.

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.53
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.53 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. obs: 48407 / % possible obs: 95.4 % / Observed criterion σ(I): 0 / Redundancy: 98.1 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 29.1
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 81.5 % / Rmerge(I) obs: 0.221 / Mean I/σ(I) obs: 9.32 / % possible all: 98.1

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GNX

1gnx


Resolution: 2.2→40 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2264 --RANDOM
Rwork0.1984 ---
obs0.1984 48395 95.3 %-
Displacement parametersBiso mean: 77.5029 Å2
Baniso -1Baniso -2Baniso -3
1--4.02 Å20 Å20 Å2
2--2.855 Å20 Å2
3---1.165 Å2
Refinement stepCycle: LAST / Resolution: 2.2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6852 0 21 514 7387
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005881
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.28587
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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