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- PDB-3fn9: Crystal structure of putative beta-galactosidase from bacteroides... -

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Basic information

Entry
Database: PDB / ID: 3fn9
TitleCrystal structure of putative beta-galactosidase from bacteroides fragilis
ComponentsPutative beta-galactosidase
KeywordsHYDROLASE / structural genomics / Putative beta-galactosidase / Glycosidase / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


beta-galactosidase / beta-galactosidase activity / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase, family 2 / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2 / Glycosyl hydrolases family 2, sugar binding domain / Beta-Galactosidase/glucuronidase domain superfamily / Galactose-binding domain-like / Galactose-binding-like domain superfamily ...Glycoside hydrolase, family 2 / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2 / Glycosyl hydrolases family 2, sugar binding domain / Beta-Galactosidase/glucuronidase domain superfamily / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Glycosidases / Glycoside hydrolase superfamily / Jelly Rolls / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Putative beta-galactosidase
Similarity search - Component
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsRamagopal, U.A. / Toro, R. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be published
Title: Structure of putative beta-galactosidase from bacteroides fragilis
Authors: Ramagopal, U.A. / Toro, R. / Burley, S.K. / Almo, S.C.
History
DepositionDec 23, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative beta-galactosidase
B: Putative beta-galactosidase
C: Putative beta-galactosidase
D: Putative beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)317,62811
Polymers317,3804
Non-polymers2487
Water1,65792
1
A: Putative beta-galactosidase
B: Putative beta-galactosidase
D: Putative beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,2479
Polymers238,0353
Non-polymers2136
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-1.7 kcal/mol
Surface area48940 Å2
MethodPISA
2
A: Putative beta-galactosidase
C: Putative beta-galactosidase
D: Putative beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,28310
Polymers238,0353
Non-polymers2487
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-1 kcal/mol
Surface area48700 Å2
MethodPISA
3
A: Putative beta-galactosidase
B: Putative beta-galactosidase
D: Putative beta-galactosidase
hetero molecules

A: Putative beta-galactosidase
C: Putative beta-galactosidase
D: Putative beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)476,53019
Polymers476,0706
Non-polymers46113
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_465-x-1/2,-y+1,z+1/21
Buried area11220 Å2
ΔGint-23.8 kcal/mol
Surface area95120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.453, 133.066, 221.192
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31D
41B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 4 / Auth seq-ID: 22 - 686 / Label seq-ID: 3 - 667

Dom-IDAuth asym-IDLabel asym-ID
1AA
2CC
3DD
4BB

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Components

#1: Protein
Putative beta-galactosidase


Mass: 79344.922 Da / Num. of mol.: 4 / Fragment: UNP residues 23-703
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Strain: NCTC 9343 / Gene: BF0029 / Plasmid: BC-pSGX4(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5LJ68, beta-galactosidase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.54 Å3/Da / Density % sol: 51.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Bis-tris pH 6.5, 25% PEG 3350, 0.2M MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 14, 2008
RadiationMonochromator: Si(111) / Protocol: SAD / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 89259 / Num. obs: 89259 / % possible obs: 100 % / Redundancy: 10.3 % / Rmerge(I) obs: 0.146 / Rsym value: 0.103 / Χ2: 1.033 / Net I/σ(I): 16.844
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.7-2.810.10.83388350.8141100
2.8-2.9110.20.63588160.841100
2.91-3.0410.30.47888370.8631100
3.04-3.210.50.31888330.9061100
3.2-3.410.60.20988600.9481100
3.4-3.6610.60.1688751.0361100
3.66-4.0310.60.12789071.1341100
4.03-4.6210.40.0989281.1771100
4.62-5.8110.10.07590341.1411100
5.81-5010.20.06593341.44199.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
CBASSdata collection
HKL-2000data reduction
SHELXDphasing
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→49.39 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.884 / WRfactor Rfree: 0.239 / WRfactor Rwork: 0.177 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.792 / SU B: 13.56 / SU ML: 0.274 / SU Rfree: 0.376 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.376 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.27 4414 5 %RANDOM
Rwork0.201 ---
obs0.204 89140 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 89.8 Å2 / Biso mean: 39.462 Å2 / Biso min: 11.2 Å2
Baniso -1Baniso -2Baniso -3
1--3.05 Å20 Å20 Å2
2--4.43 Å20 Å2
3----1.38 Å2
Refinement stepCycle: LAST / Resolution: 2.7→49.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21641 0 7 92 21740
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02222245
X-RAY DIFFRACTIONr_angle_refined_deg1.3631.92830232
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.58352679
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.31624.1371112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.753153598
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.86215115
X-RAY DIFFRACTIONr_chiral_restr0.0880.23160
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02117306
X-RAY DIFFRACTIONr_mcbond_it1.297213307
X-RAY DIFFRACTIONr_mcangle_it2.209321447
X-RAY DIFFRACTIONr_scbond_it1.48828938
X-RAY DIFFRACTIONr_scangle_it2.28538785
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 5336 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
AMEDIUM POSITIONAL0.370.5
BMEDIUM POSITIONAL0.330.5
CMEDIUM POSITIONAL0.360.5
DMEDIUM POSITIONAL0.380.5
AMEDIUM THERMAL2.372
BMEDIUM THERMAL3.72
CMEDIUM THERMAL2.312
DMEDIUM THERMAL3.562
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.42 319 -
Rwork0.292 6173 -
all-6492 -
obs--99.25 %

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