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- PDB-1v7v: Crystal structure of Vibrio proteolyticus chitobiose phosphorylase -

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Basic information

Entry
Database: PDB / ID: 1v7v
TitleCrystal structure of Vibrio proteolyticus chitobiose phosphorylase
Componentschitobiose phosphorylase
KeywordsTRANSFERASE / beta-sandwich / (alpha/alpha)6 barrel
Function / homology
Function and homology information


N,N'-diacetylchitobiose phosphorylase / transferase activity / carbohydrate binding / carbohydrate metabolic process / metal ion binding
Similarity search - Function
N,N'-diacetylchitobiose phosphorylase, N-terminal / Putative carbohydrate binding domain / Putative carbohydrate binding domain / Glycoside hydrolase, family 65, N-terminal domain / Maltose phosphorylase, domain 3 / Maltose phosphorylase, domain 3 / Glycosyl hydrolase 94 / Glycosyltransferase family 36 / Glycosyl hydrolase 36, catalytic domain / Glycosyl hydrolase 36 superfamily, catalytic domain ...N,N'-diacetylchitobiose phosphorylase, N-terminal / Putative carbohydrate binding domain / Putative carbohydrate binding domain / Glycoside hydrolase, family 65, N-terminal domain / Maltose phosphorylase, domain 3 / Maltose phosphorylase, domain 3 / Glycosyl hydrolase 94 / Glycosyltransferase family 36 / Glycosyl hydrolase 36, catalytic domain / Glycosyl hydrolase 36 superfamily, catalytic domain / Glycoside hydrolase family 65, N-terminal domain superfamily / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Galactose mutarotase-like domain superfamily / Beta-galactosidase; Chain A, domain 5 / Glycosyltransferase / Alpha/alpha barrel / Distorted Sandwich / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
N,N'-diacetylchitobiose phosphorylase
Similarity search - Component
Biological speciesVibrio proteolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsHidaka, M. / Honda, Y. / Nirasawa, S. / Kitaoka, M. / Hayashi, K. / Wakagi, T. / Shoun, H. / Fushinobu, S.
Citation
Journal: Structure / Year: 2004
Title: Chitobiose phosphorylase from Vibrio proteolyticus, a member of glycosyl transferase family 36, has a clan GH-L-like (alpha/alpha)(6) barrel fold.
Authors: Hidaka, M. / Honda, Y. / Kitaoka, M. / Nirasawa, S. / Hayashi, K. / Wakagi, T. / Shoun, H. / Fushinobu, S.
#1: Journal: Biochem.J. / Year: 2004
Title: Reaction mechanism of chitobiose phosphorylase from Vibrio proteolyticus: identification of family 36 glycosyltransferase in Vibrio
Authors: Honda, Y. / Kitaoka, M. / Hayashi, K.
History
DepositionDec 24, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 22, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: chitobiose phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,4064
Polymers91,2861
Non-polymers1203
Water12,178676
1
A: chitobiose phosphorylase
hetero molecules

A: chitobiose phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,8128
Polymers182,5722
Non-polymers2406
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area5900 Å2
ΔGint-72 kcal/mol
Surface area49520 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)140.946, 70.580, 80.045
Angle α, β, γ (deg.)90.00, 98.40, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a dimer generated from the monomer in the asymmetric unit by the operations: 1-x, y, 1-z.

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Components

#1: Protein chitobiose phosphorylase


Mass: 91285.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio proteolyticus (bacteria) / Gene: chbp / Plasmid: pET30b-ChBP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21GOLD(DE3)
References: UniProt: Q76IQ9, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 676 / 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: 2.04 Å3/Da / Density % sol: 39.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG400, HEPES, Calcium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1.0000, 0.97120, 0.97848, 0.97960
DetectorType: ACSC QUANTUM 210 / Detector: CCD / Date: Jun 23, 2003
RadiationMonochromator: Double-crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97121
30.978481
40.97961
ReflectionResolution: 1.8→50 Å / Num. all: 71854 / Num. obs: 70781 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 13.3 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 15.3
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2 % / Rmerge(I) obs: 0.228 / Mean I/σ(I) obs: 5.33 / Num. unique all: 6987 / Rsym value: 0.228 / % possible all: 97.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→47.78 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2109709.68 / Data cutoff low absF: 0 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.186 3588 5.1 %RANDOM
Rwork0.162 ---
all0.163 71854 --
obs0.162 70781 98.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.5526 Å2 / ksol: 0.379537 e/Å3
Displacement parametersBiso mean: 18.9 Å2
Baniso -1Baniso -2Baniso -3
1--3.38 Å20 Å20.37 Å2
2--3.32 Å20 Å2
3---0.05 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.8→47.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6222 0 3 676 6901
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.371.5
X-RAY DIFFRACTIONc_mcangle_it1.872
X-RAY DIFFRACTIONc_scbond_it2.452
X-RAY DIFFRACTIONc_scangle_it3.542.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.225 571 5 %
Rwork0.185 10863 -
obs-6987 95.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMION.TOP
X-RAY DIFFRACTION3ION.PARAMWATER.TOP
X-RAY DIFFRACTION4CIS_PEPTIDE.PARAM

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