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- PDB-2zus: Crystal structure of Galacto-N-biose/Lacto-N-biose I phosphorylase -

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Basic information

Entry
Database: PDB / ID: 2zus
TitleCrystal structure of Galacto-N-biose/Lacto-N-biose I phosphorylase
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
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: 2.11 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: Version format compliance
Revision 1.2Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_residues / software
Revision 1.3Mar 13, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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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)341,9856
Polymers341,9364
Non-polymers492
Water34,1921898
1
A: Lacto-N-biose phosphorylase
B: Lacto-N-biose phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,9923
Polymers170,9682
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6580 Å2
ΔGint-19 kcal/mol
Surface area52160 Å2
MethodPISA
2
C: Lacto-N-biose phosphorylase
D: Lacto-N-biose phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,9923
Polymers170,9682
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6600 Å2
ΔGint-19 kcal/mol
Surface area51810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.764, 111.483, 118.793
Angle α, β, γ (deg.)105.130, 90.220, 107.780
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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1898 / 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: 48.8 % / Mosaicity: 0.668 °
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.5
Details: Na cacodyrate, Mg(NO3)2, PEG 4000, 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 BL-5A11
SYNCHROTRONPhoton Factory BL-5A20.97934, 0.97974, 0.96450
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDDec 14, 2006
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: 2.1→50 Å / Num. all: 344949 / Num. obs: 178361 / % possible obs: 97.7 % / Redundancy: 1.9 % / Biso Wilson estimate: 26.9 Å2 / Rmerge(I) obs: 0.052 / Χ2: 1.05 / Net I/σ(I): 15.833
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 3.2 / Num. unique all: 17539 / Χ2: 0.798 / % possible all: 95.9

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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: 2.11→32.12 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.921 / WRfactor Rfree: 0.217 / WRfactor Rwork: 0.164 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.871 / SU R Cruickshank DPI: 0.227 / SU Rfree: 0.189 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.227 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.225 8945 5 %RANDOM
Rwork0.17 ---
obs0.173 178358 96.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 89.13 Å2 / Biso mean: 27.937 Å2 / Biso min: 9.99 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å2-0.01 Å20 Å2
2---0.05 Å2-0.01 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.211 Å
Refinement stepCycle: LAST / Resolution: 2.11→32.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23724 0 2 1898 25624
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02224393
X-RAY DIFFRACTIONr_angle_refined_deg1.3291.93433222
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.08252972
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.03223.8071245
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.206153701
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.86315164
X-RAY DIFFRACTIONr_chiral_restr0.0960.23503
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02119282
X-RAY DIFFRACTIONr_mcbond_it0.6531.514811
X-RAY DIFFRACTIONr_mcangle_it1.156223872
X-RAY DIFFRACTIONr_scbond_it1.84739582
X-RAY DIFFRACTIONr_scangle_it2.794.59350
LS refinement shellResolution: 2.107→2.161 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 618 -
Rwork0.193 10924 -
all-11542 -
obs--85.47 %

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