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- PDB-3cmg: Crystal structure of putative beta-galactosidase from Bacteroides... -

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Basic information

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


beta-glucuronidase / beta-galactosidase activity / carbohydrate metabolic process
Similarity search - Function
Domain of unknown function DUF4982 / Domain of unknown function (DUF4982) / 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 ...Domain of unknown function DUF4982 / Domain of unknown function (DUF4982) / 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
PHOSPHATE ION / Beta-glucuronidase
Similarity search - Component
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsRamagopal, U.A. / Rutter, M. / Toro, R. / Hu, S. / Maletic, M. / Gheyi, T. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be published
Title: Crystal structure of putative beta-galactosidase from Bacteroides fragilis.
Authors: Ramagopal, U.A. / Rutter, M. / Toro, R. / Hu, S. / Maletic, M. / Gheyi, T. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionMar 21, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 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 1.3Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 3, 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 1.5Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,1736
Polymers76,6881
Non-polymers4855
Water9,512528
1
A: Putative beta-galactosidase
hetero molecules

A: Putative beta-galactosidase
hetero molecules

A: Putative beta-galactosidase
hetero molecules

A: Putative beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)308,69324
Polymers306,7544
Non-polymers1,94020
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area14080 Å2
ΔGint-5.4 kcal/mol
Surface area92360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.651, 102.878, 199.967
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-840-

HOH

21A-860-

HOH

31A-892-

HOH

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Components

#1: Protein Putative beta-galactosidase


Mass: 76688.391 Da / Num. of mol.: 1 / Fragment: Residues 38-693
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Strain: NCTC 9343 / Gene: BF0328 / Plasmid: BC-pSGX4(BC) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5LIC7
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 528 / 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: 2.67 Å3/Da / Density % sol: 53.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris-HCl pH 8.5, 50% MPD, 0.22M Ammonium dihydrogen phosphate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X29A10.979
SYNCHROTRONNSLS X6A20.979
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDMar 6, 2008
ADSC QUANTUM 3152CCDMar 5, 2008
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 124005 / Num. obs: 124005 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.088 / Rsym value: 0.065 / Χ2: 0.658 / Net I/σ(I): 5.6
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.423 / Mean I/σ(I) obs: 2.4 / Num. unique all: 11983 / Rsym value: 0.337 / Χ2: 0.418 / % possible all: 96.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
CBASSdata collection
HKL-2000data reduction
SHELXEmodel building
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→39.84 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.614 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.115 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: The Friedel pairs were used in phasing
RfactorNum. reflection% reflectionSelection details
Rfree0.186 3256 5.1 %RANDOM
Rwork0.148 ---
all0.15 64465 --
obs0.15 64465 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.874 Å2
Baniso -1Baniso -2Baniso -3
1-3.38 Å20 Å20 Å2
2---0.96 Å20 Å2
3----2.41 Å2
Refinement stepCycle: LAST / Resolution: 1.9→39.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5357 0 30 528 5915
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225599
X-RAY DIFFRACTIONr_angle_refined_deg1.3761.9377611
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.445679
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.16623.979289
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.57615930
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6231537
X-RAY DIFFRACTIONr_chiral_restr0.1020.2793
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024366
X-RAY DIFFRACTIONr_nbd_refined0.1980.32389
X-RAY DIFFRACTIONr_nbtor_refined0.3190.53762
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.5858
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1720.342
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2070.556
X-RAY DIFFRACTIONr_mcbond_it2.51623413
X-RAY DIFFRACTIONr_mcangle_it3.41835382
X-RAY DIFFRACTIONr_scbond_it3.05622518
X-RAY DIFFRACTIONr_scangle_it4.36732224
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 249 -
Rwork0.196 4301 -
all-4550 -
obs--95.93 %

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