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- PDB-2zuu: Crystal structure of Galacto-N-biose/Lacto-N-biose I phosphorylas... -

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Basic information

Entry
Database: PDB / ID: 2zuu
TitleCrystal structure of Galacto-N-biose/Lacto-N-biose I phosphorylase in complex with GlcNAc
ComponentsLacto-N-biose phosphorylase
KeywordsTRANSFERASE / beta-alpha-barrel / TIM barrel / Glycosyltransferase
Function / homology
Function and homology information


1,3-beta-galactosyl-N-acetylhexosamine phosphorylase / 1,3-beta-galactosyl-N-acetylhexosamine phosphorylase activity / 1,4-alpha-oligoglucan phosphorylase activity / carbohydrate metabolic process
Similarity search - Function
Lacto-N-biose phosphorylase/D-galactosyl-beta-1->4-L-rhamnose phosphorylase / Lacto-N-biose phosphorylase-like, N-terminal TIM barrel domain / Lacto-N-biose phosphorylase, C-terminal domain / Lacto-N-biose phosphorylase, central domain / Lacto-N-biose phosphorylase N-terminal TIM barrel domain / Lacto-N-biose phosphorylase central domain / Lacto-N-biose phosphorylase C-terminal domain / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Golgi alpha-mannosidase II ...Lacto-N-biose phosphorylase/D-galactosyl-beta-1->4-L-rhamnose phosphorylase / Lacto-N-biose phosphorylase-like, N-terminal TIM barrel domain / Lacto-N-biose phosphorylase, C-terminal domain / Lacto-N-biose phosphorylase, central domain / Lacto-N-biose phosphorylase N-terminal TIM barrel domain / Lacto-N-biose phosphorylase central domain / Lacto-N-biose phosphorylase C-terminal domain / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
2-acetamido-2-deoxy-alpha-D-glucopyranose / 1,3-beta-galactosyl-N-acetylhexosamine phosphorylase / 1,3-beta-galactosyl-N-acetylhexosamine phosphorylase
Similarity search - Component
Biological speciesBifidobacterium longum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHidaka, M. / Nishimoto, M. / Kitaoka, M. / Wakagi, T. / Shoun, H. / Fushinobu, S.
Citation
Journal: J.Biol.Chem. / Year: 2009
Title: The crystal structure of galacto-N-biose/lacto-N-biose I phosphorylase: A large deformation of a tim barrel scaffold
Authors: Hidaka, M. / Nishimoto, M. / Kitaoka, M. / Wakagi, T. / Shoun, H. / Fushinobu, S.
#1: Journal: Appl.Environ.Microbiol. / Year: 2005
Title: Novel putative galactose operon involving lacto-N-biose phosphorylase in Bifidobacterium longum
Authors: Kitaoka, M. / Tian, J. / Nishimoto, M.
History
DepositionOct 28, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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.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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lacto-N-biose phosphorylase
B: Lacto-N-biose phosphorylase
C: Lacto-N-biose phosphorylase
D: Lacto-N-biose phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)343,21413
Polymers341,9364
Non-polymers1,2789
Water29,5091638
1
A: Lacto-N-biose phosphorylase
B: Lacto-N-biose phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,6197
Polymers170,9682
Non-polymers6515
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8130 Å2
ΔGint-9 kcal/mol
Surface area51450 Å2
MethodPISA
2
C: Lacto-N-biose phosphorylase
D: Lacto-N-biose phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,5956
Polymers170,9682
Non-polymers6274
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8040 Å2
ΔGint-5 kcal/mol
Surface area51630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.777, 111.484, 118.432
Angle α, β, γ (deg.)105.190, 90.480, 107.350
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Lacto-N-biose phosphorylase / Galacto-N-biose/lacto-N-biose I phosphorylase


Mass: 85484.062 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium longum (bacteria) / Strain: JCM1217 / Gene: lnpA / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q5NU17, UniProt: E8MF13*PLUS, 1,3-beta-galactosyl-N-acetylhexosamine phosphorylase
#2: Sugar
ChemComp-NDG / 2-acetamido-2-deoxy-alpha-D-glucopyranose / N-acetyl-alpha-D-glucosamine / 2-acetamido-2-deoxy-alpha-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-glucopyranosamineCOMMON NAMEGMML 1.0
a-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1638 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.75 % / Mosaicity: 0.946 °
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.5
Details: Na cacodyrate, Mg(NO3)2, PEG 4000, GlcNAc, pH 6.5, VAPOR DIFFUSION, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1951
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory AR-NW12A11
SYNCHROTRONPhoton Factory BL-5A20.97934, 0.97974, 0.96450
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDJan 28, 2007
ADSC QUANTUM 3152CCDNov 29, 2006
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.979341
30.979741
40.96451
ReflectionResolution: 2.3→50 Å / Num. all: 269456 / Num. obs: 137195 / % possible obs: 97.8 % / Redundancy: 2 % / Biso Wilson estimate: 35.8 Å2 / Rmerge(I) obs: 0.054 / Χ2: 1.072 / Net I/σ(I): 15.293
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2 % / Rmerge(I) obs: 0.246 / Mean I/σ(I) obs: 2.5 / Num. unique all: 13720 / Χ2: 0.641 / % possible all: 97.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→40.68 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.921 / WRfactor Rfree: 0.216 / WRfactor Rwork: 0.16 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.848 / SU R Cruickshank DPI: 0.374 / SU Rfree: 0.24 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.374 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.231 6869 5 %RANDOM
Rwork0.17 ---
obs0.173 137184 97.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 85.76 Å2 / Biso mean: 35.174 Å2 / Biso min: 11.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20.27 Å2-0.04 Å2
2--0.27 Å20.01 Å2
3----0.36 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: LAST / Resolution: 2.3→40.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23549 0 85 1638 25272
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02224296
X-RAY DIFFRACTIONr_angle_refined_deg1.2181.93733085
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.87652951
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.85123.7711233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.843153675
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.31215164
X-RAY DIFFRACTIONr_chiral_restr0.0850.23495
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02119161
X-RAY DIFFRACTIONr_mcbond_it0.5051.514703
X-RAY DIFFRACTIONr_mcangle_it0.969223698
X-RAY DIFFRACTIONr_scbond_it1.48139593
X-RAY DIFFRACTIONr_scangle_it2.4014.59387
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 412 -
Rwork0.23 8769 -
all-9181 -
obs--87.67 %

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