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- PDB-1v7x: Crystal structure of Vibrio proteolyticus chitobiose phosphorylas... -

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Basic information

Entry
Database: PDB / ID: 1v7x
TitleCrystal structure of Vibrio proteolyticus chitobiose phosphorylase in complex with GlcNAc and sulfate
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
2-acetamido-2-deoxy-alpha-D-glucopyranose / N,N'-diacetylchitobiose phosphorylase
Similarity search - Component
Biological speciesVibrio proteolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 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
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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)91,9056
Polymers91,2861
Non-polymers6195
Water9,962553
1
A: chitobiose phosphorylase
hetero molecules

A: chitobiose phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,80912
Polymers182,5722
Non-polymers1,23710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area8350 Å2
ΔGint-66 kcal/mol
Surface area47490 Å2
MethodPISA, PQS
Unit cell
γ
α
β
Length a, b, c (Å)140.871, 70.355, 79.939
Angle α, β, γ (deg.)90.00, 98.36, 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

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Protein , 1 types, 1 molecules A

#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

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Sugars , 2 types, 2 molecules

#2: Sugar ChemComp-NDG / 2-acetamido-2-deoxy-alpha-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 1
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: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 556 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 553 / 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: 2.06 Å3/Da / Density % sol: 39.67 %
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: Oct 17, 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: 2→50 Å / Num. all: 52234 / Num. obs: 52164 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 11.9 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Net I/σ(I): 9.5
Reflection shellHighest resolution: 2 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.271 / Mean I/σ(I) obs: 3.31 / Num. unique all: 5200 / Rsym value: 0.271 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2→47.69 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2461464.32 / 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
Rfree0.195 2599 5 %RANDOM
Rwork0.163 ---
all0.165 52234 --
obs0.163 52164 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.8656 Å2 / ksol: 0.383753 e/Å3
Displacement parametersBiso mean: 22.5 Å2
Baniso -1Baniso -2Baniso -3
1--7.2 Å20 Å20.46 Å2
2--7.2 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 2→47.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6222 0 37 553 6812
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_d23.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.531.5
X-RAY DIFFRACTIONc_mcangle_it2.032
X-RAY DIFFRACTIONc_scbond_it2.632
X-RAY DIFFRACTIONc_scangle_it3.622.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.234 424 5 %
Rwork0.19 8097 -
obs-5200 98.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMION.TOP
X-RAY DIFFRACTION3NAG.PARAMNAG.TOP
X-RAY DIFFRACTION4CIS_PEPTIDE.PARAMWATER.TOP
X-RAY DIFFRACTION5ION.PARAM

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