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- PDB-2xhy: Crystal Structure of E.coli BglA -

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Basic information

Entry
Database: PDB / ID: 2xhy
TitleCrystal Structure of E.coli BglA
Components6-PHOSPHO-BETA-GLUCOSIDASE BGLA
KeywordsHYDROLASE / GLYCOSIDASE
Function / homology
Function and homology information


6-phospho-beta-glucosidase / 6-phospho-beta-glucosidase activity / : / glucosidase activity / carbohydrate catabolic process / beta-glucosidase activity / cytosol
Similarity search - Function
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
BROMIDE ION / 6-phospho-beta-glucosidase BglA
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsTotir, M. / Zubieta, C. / Echols, N. / May, A.P. / Gee, C.L. / nanao, M. / alber, T.
CitationJournal: Plos One / Year: 2012
Title: Macro-to-Micro Structural Proteomics: Native Source Proteins for High-Throughput Crystallization.
Authors: Totir, M. / Echols, N. / Nanao, M. / Gee, C.L. / Moskaleva, A. / Gradia, S. / Iavarone, A.T. / Berger, J.M. / May, A.P. / Zubieta, C. / Alber, T.
History
DepositionJun 24, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Database references / Structure summary / Version format compliance
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "CA" 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: 6-PHOSPHO-BETA-GLUCOSIDASE BGLA
B: 6-PHOSPHO-BETA-GLUCOSIDASE BGLA
C: 6-PHOSPHO-BETA-GLUCOSIDASE BGLA
D: 6-PHOSPHO-BETA-GLUCOSIDASE BGLA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,70928
Polymers221,7104
Non-polymers1,99824
Water29,6891648
1
C: 6-PHOSPHO-BETA-GLUCOSIDASE BGLA
D: 6-PHOSPHO-BETA-GLUCOSIDASE BGLA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,84614
Polymers110,8552
Non-polymers99112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5220 Å2
ΔGint-59.5 kcal/mol
Surface area34300 Å2
MethodPISA
2
A: 6-PHOSPHO-BETA-GLUCOSIDASE BGLA
B: 6-PHOSPHO-BETA-GLUCOSIDASE BGLA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,86314
Polymers110,8552
Non-polymers1,00712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5650 Å2
ΔGint-77.4 kcal/mol
Surface area34800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.674, 79.424, 98.604
Angle α, β, γ (deg.)99.96, 107.21, 102.83
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.007992, 0.6234, -0.7819), (0.6293, -0.6045, -0.4884), (-0.7771, -0.496, -0.3875)
Vector: 37.38, 62.28, 97.55)

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Components

#1: Protein
6-PHOSPHO-BETA-GLUCOSIDASE BGLA / BGLA


Mass: 55427.590 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: K-12 / References: UniProt: Q46829, 6-phospho-beta-glucosidase
#2: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: Br
#3: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 1648 / 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: 2.34 Å3/Da / Density % sol: 47.5 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.92004
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 25, 2008
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92004 Å / Relative weight: 1
ReflectionResolution: 2.3→22.9 Å / Num. obs: 83032 / % possible obs: 92.7 % / Observed criterion σ(I): -10 / Redundancy: 4 % / Biso Wilson estimate: 19.95 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 7.9
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.2 / % possible all: 66.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.6_289)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XK6

1xk6


Resolution: 2.3→22.94 Å / SU ML: 0.36 / σ(F): 1.96 / Phase error: 23.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.236 4153 5 %
Rwork0.171 --
obs0.174 82815 92.7 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.76 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.1095 Å20.5992 Å2-0.6773 Å2
2--0.5269 Å21.3906 Å2
3---0.5827 Å2
Refinement stepCycle: LAST / Resolution: 2.3→22.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15278 0 44 1648 16970
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00315755
X-RAY DIFFRACTIONf_angle_d0.70421324
X-RAY DIFFRACTIONf_dihedral_angle_d15.9985613
X-RAY DIFFRACTIONf_chiral_restr0.0542121
X-RAY DIFFRACTIONf_plane_restr0.0022763
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.32610.3222890.23941614X-RAY DIFFRACTION57
2.3261-2.35350.32041000.23171739X-RAY DIFFRACTION62
2.3535-2.38210.27471040.23031886X-RAY DIFFRACTION68
2.3821-2.41230.32931290.2322070X-RAY DIFFRACTION74
2.4123-2.4440.31151210.22312330X-RAY DIFFRACTION83
2.444-2.47740.29761440.23052723X-RAY DIFFRACTION95
2.4774-2.51280.36571440.23212732X-RAY DIFFRACTION97
2.5128-2.55020.29891560.21112742X-RAY DIFFRACTION97
2.5502-2.590.29671570.19562721X-RAY DIFFRACTION97
2.59-2.63240.27731470.19412761X-RAY DIFFRACTION97
2.6324-2.67770.28711350.2072744X-RAY DIFFRACTION97
2.6777-2.72640.2571340.19612813X-RAY DIFFRACTION97
2.7264-2.77870.31341470.19572664X-RAY DIFFRACTION97
2.7787-2.83530.25331270.18642829X-RAY DIFFRACTION97
2.8353-2.89690.24361360.18912754X-RAY DIFFRACTION97
2.8969-2.96410.26561380.17992758X-RAY DIFFRACTION97
2.9641-3.03810.2581370.17542778X-RAY DIFFRACTION98
3.0381-3.120.2371440.17032725X-RAY DIFFRACTION98
3.12-3.21160.22971420.16822791X-RAY DIFFRACTION98
3.2116-3.3150.24931480.16472767X-RAY DIFFRACTION98
3.315-3.43310.2241470.15682745X-RAY DIFFRACTION98
3.4331-3.570.19961450.13132763X-RAY DIFFRACTION98
3.57-3.73190.19081700.12592756X-RAY DIFFRACTION98
3.7319-3.92770.18481410.12622754X-RAY DIFFRACTION98
3.9277-4.17240.17931460.11862810X-RAY DIFFRACTION98
4.1724-4.49230.17121400.11782752X-RAY DIFFRACTION98
4.4923-4.94030.1591490.1172806X-RAY DIFFRACTION98
4.9403-5.64590.21021410.13732767X-RAY DIFFRACTION98
5.6459-7.07840.2211460.15352774X-RAY DIFFRACTION98
7.0784-22.94120.16351490.15492794X-RAY DIFFRACTION98

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