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- PDB-2vtf: X-ray crystal structure of the Endo-beta-N-acetylglucosaminidase ... -

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Basic information

Entry
Database: PDB / ID: 2vtf
TitleX-ray crystal structure of the Endo-beta-N-acetylglucosaminidase from Arthrobacter protophormiae E173Q mutant reveals a TIM barrel catalytic domain and two ancillary domains
ComponentsENDO-BETA-N-ACETYLGLUCOSAMINIDASE
KeywordsHYDROLASE / FAMILY 85 / GLYCOSIDASE / ARTHROBACTER / CARBOHYDRATE BINDING / ACETYLGLUCOSAMINIDASE
Function / homology
Function and homology information


mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase / mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity / carbohydrate metabolic process / metal ion binding / cytosol
Similarity search - Function
Glycoside hydrolase, family 85 / Cytosolic endo-beta-N-acetylglucosaminidase / : / Glycosyl hydrolase family 85 / GH85 endohexosaminidases, C-terminal domain / Galactose-binding domain-like / Glycosidases / Jelly Rolls / TIM Barrel / Alpha-Beta Barrel ...Glycoside hydrolase, family 85 / Cytosolic endo-beta-N-acetylglucosaminidase / : / Glycosyl hydrolase family 85 / GH85 endohexosaminidases, C-terminal domain / Galactose-binding domain-like / Glycosidases / Jelly Rolls / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Endo-beta-N-acetylglucosaminidase
Similarity search - Component
Biological speciesARTHROBACTER PROTOPHORMIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.79 Å
AuthorsLing, Z. / Bingham, R.J. / Suits, M.D.L. / Moir, J.W.B. / Fairbanks, A.J. / Taylor, E.J.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: The X-Ray Crystal Structure of an Arthrobacter Protophormiae Endo-Beta-N-Acetylglucosaminidase Reveals a (Beta/Alpha)(8) Catalytic Domain, Two Ancillary Domains and Active Site Residues Key ...Title: The X-Ray Crystal Structure of an Arthrobacter Protophormiae Endo-Beta-N-Acetylglucosaminidase Reveals a (Beta/Alpha)(8) Catalytic Domain, Two Ancillary Domains and Active Site Residues Key for Transglycosylation Activity.
Authors: Suits, M.D. / Ling, Z. / Bingham, R.J. / Bruce, N.C. / Davies, G.J. / Fairbanks, A.J. / Moir, J.W. / Taylor, E.J.
History
DepositionMay 14, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ENDO-BETA-N-ACETYLGLUCOSAMINIDASE
B: ENDO-BETA-N-ACETYLGLUCOSAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,89510
Polymers140,1652
Non-polymers1,7308
Water27,0231500
1
A: ENDO-BETA-N-ACETYLGLUCOSAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9475
Polymers70,0821
Non-polymers8654
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ENDO-BETA-N-ACETYLGLUCOSAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9475
Polymers70,0821
Non-polymers8654
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)89.840, 226.760, 68.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein ENDO-BETA-N-ACETYLGLUCOSAMINIDASE


Mass: 70082.422 Da / Num. of mol.: 2 / Fragment: RESIDUES 25-645 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARTHROBACTER PROTOPHORMIAE (bacteria) / Strain: AKU0647 / Plasmid: PET23D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9ZB22, mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase
#2: Chemical
ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#3: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1500 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASN 67 TO ASP ENGINEERED RESIDUE IN CHAIN A, LYS 75 TO THR ...ENGINEERED RESIDUE IN CHAIN A, ASN 67 TO ASP ENGINEERED RESIDUE IN CHAIN A, LYS 75 TO THR ENGINEERED RESIDUE IN CHAIN A, GLU 197 TO GLN ENGINEERED RESIDUE IN CHAIN B, ASN 67 TO ASP ENGINEERED RESIDUE IN CHAIN B, LYS 75 TO THR ENGINEERED RESIDUE IN CHAIN B, GLU 197 TO GLN

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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: 2.52 Å3/Da / Density % sol: 51.22 % / Description: NONE
Crystal growpH: 6.5
Details: 0.35 M KSCN, 0.1 M BIS-TRIS PROPANE (PH 6.5), 15% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9765
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 9, 2007 / Details: ORODIAL FOCUSING MIRROR
RadiationMonochromator: SI111 CHANNEL CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 1.8→80 Å / Num. obs: 130527 / % possible obs: 99.9 % / Observed criterion σ(I): 5 / Redundancy: 5.7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 23
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.7 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.4.0077refinement
HKL-2000data reduction
SCALEPACKdata scaling
autoSHARPphasing
SOLOMONphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1.79→49.03 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.814 / SU ML: 0.069 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SER207 IS A RAMACHANDRAN PLOT OUTLIER AND IMPORTANT ACTIVE SITE RESIDUE THAT INTERACTS WITH THE CATALYTIC ACID/BASE.
RfactorNum. reflection% reflectionSelection details
Rfree0.202 6652 5 %RANDOM
Rwork0.164 ---
obs0.166 125475 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.79→49.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9685 0 112 1500 11297
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02110218
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2481.92513941
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.43951255
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.72724.867528
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.081151467
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6031541
X-RAY DIFFRACTIONr_chiral_restr0.0910.21415
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218154
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6321.56187
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.18429914
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.90234031
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1014.54027
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.79→1.84 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 493 -
Rwork0.216 9162 -
obs--99.96 %
Refinement TLS params.Method: refined / Origin x: 37.2598 Å / Origin y: -25.9044 Å / Origin z: -26.0834 Å
111213212223313233
T0.0205 Å2-0.0193 Å2-0.0065 Å2-0.0205 Å20.004 Å2--0.0218 Å2
L0.1219 °2-0.0805 °2-0.0406 °2-0.0542 °20.034 °2--0.0641 °2
S-0.0046 Å °-0.0073 Å °0.0075 Å °0.0171 Å °-0.0024 Å °-0.0167 Å °0.0282 Å °-0.0153 Å °0.0069 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 617
2X-RAY DIFFRACTION1B2 - 619

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