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- PDB-2chn: Bacteroides thetaiotaomicron hexosaminidase with O-GlcNAcase acti... -

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Basic information

Entry
Database: PDB / ID: 2chn
TitleBacteroides thetaiotaomicron hexosaminidase with O-GlcNAcase activity- NAG-thiazoline complex
Components(GLUCOSAMINIDASE) x 2
KeywordsHYDROLASE / O-GLCNACASE / N-ACETYLGLUCOSAMIBE
Function / homology
Function and homology information


protein O-GlcNAcase / protein deglycosylation / [protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine/L-threonine O-N-acetyl-alpha-D-glucosaminase activity / beta-N-acetylglucosaminidase activity / carbohydrate metabolic process / identical protein binding
Similarity search - Function
: / : / Carbohydrate binding module family 32 / Bacterial GH84, post-catalytic domain / Hyaluronidase post-catalytic domain-like / Beta-N-acetylglucosaminidase / beta-N-acetylglucosaminidase / Glycosyl hydrolases family 84 (GH84) domain profile. / : / Chitobiase/beta-hexosaminidase domain 2-like ...: / : / Carbohydrate binding module family 32 / Bacterial GH84, post-catalytic domain / Hyaluronidase post-catalytic domain-like / Beta-N-acetylglucosaminidase / beta-N-acetylglucosaminidase / Glycosyl hydrolases family 84 (GH84) domain profile. / : / Chitobiase/beta-hexosaminidase domain 2-like / Beta-hexosaminidase, bacterial type, N-terminal / Glycosyl hydrolase family 20, domain 2 / Chitobiase; domain 2 / Beta-hexosaminidase-like, domain 2 / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Up-down Bundle / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-NGT / O-GlcNAcase BT_4395
Similarity search - Component
Biological speciesBACTEROIDES THETAIOTAOMICRON (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsDennis, R.J. / Taylor, E.J. / Macauley, M.S. / Stubbs, K.A. / Turkenburg, J.P. / Hart, S.J. / Black, G.N. / Vocadlo, D.J. / Davies, G.J.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2006
Title: Structure and Mechanism of a Bacterial B-Glucosaminidase Having O-Glcnacase Activity
Authors: Dennis, R.J. / Taylor, E.J. / Macauley, M.S. / Stubbs, K.A. / Turkenburg, J.P. / Hart, S.J. / Black, G.N. / Vocadlo, D.J. / Davies, G.J.
History
DepositionMar 15, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2006Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _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.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.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_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_conn.ptnr2_label_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 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-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 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-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: GLUCOSAMINIDASE
B: GLUCOSAMINIDASE
C: GLUCOSAMINIDASE
D: GLUCOSAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,12712
Polymers168,2394
Non-polymers8878
Water19,8711103
1
A: GLUCOSAMINIDASE
C: GLUCOSAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,5636
Polymers84,1202
Non-polymers4444
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: GLUCOSAMINIDASE
D: GLUCOSAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,5636
Polymers84,1202
Non-polymers4444
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)51.714, 94.544, 99.479
Angle α, β, γ (deg.)75.34, 93.86, 77.07
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 999
2114B1 - 999

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

#1: Protein GLUCOSAMINIDASE / HEXOSAMINIASE


Mass: 83080.469 Da / Num. of mol.: 2 / Fragment: RESIDUES 22-737
Source method: isolated from a genetically manipulated source
Details: THIAZOLINE INHIBITOR PRESENT
Source: (gene. exp.) BACTEROIDES THETAIOTAOMICRON (bacteria)
Strain: VPI-5482 / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q89ZI2, beta-N-acetylhexosaminidase
#2: Protein/peptide GLUCOSAMINIDASE / HEXOSAMINIASE


Mass: 1039.273 Da / Num. of mol.: 2 / Fragment: C TERMINUS, RESIDUES 650-653,660-668
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACTEROIDES THETAIOTAOMICRON (bacteria)
Strain: VPI-5482 / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: beta-N-acetylhexosaminidase

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Non-polymers , 4 types, 1111 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-NGT / 3AR,5R,6S,7R,7AR-5-HYDROXYMETHYL-2-METHYL-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D]THIAZOLE-6,7-DIOL


Mass: 219.258 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H13NO4S
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1103 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsRESIDUES IN DISORDERED C TERMINUS MODELLED AS POLYALANINE CHAINS C AND D ARE THE UNKNOWN RESIDUES ...RESIDUES IN DISORDERED C TERMINUS MODELLED AS POLYALANINE CHAINS C AND D ARE THE UNKNOWN RESIDUES OF THE C TERMINUS OF CHAINS A AND B

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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: 2.76 Å3/Da / Density % sol: 55.1 %
Crystal growpH: 6
Details: 0.5M NA ACETATE, 15% PEG 3500, 0.1M MES PH6, 20% GLYCEROL, pH 6.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9795
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 117950 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 12
Reflection shellResolution: 1.95→2 Å / Redundancy: 4 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.95→39.84 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.849 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.226 6255 5 %RANDOM
Rwork0.185 ---
obs0.187 117960 96.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.38 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20.01 Å2-0.01 Å2
2--0 Å20.05 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.95→39.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10531 0 54 1103 11688
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02210900
X-RAY DIFFRACTIONr_bond_other_d0.0020.027446
X-RAY DIFFRACTIONr_angle_refined_deg1.5481.95714785
X-RAY DIFFRACTIONr_angle_other_deg0.96318189
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.15651311
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.82924.878531
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.994151870
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1161550
X-RAY DIFFRACTIONr_chiral_restr0.0890.21584
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212013
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022143
X-RAY DIFFRACTIONr_nbd_refined0.2130.22190
X-RAY DIFFRACTIONr_nbd_other0.190.27655
X-RAY DIFFRACTIONr_nbtor_refined0.1790.25190
X-RAY DIFFRACTIONr_nbtor_other0.0890.25335
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2877
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0880.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2330.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1630.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0831.56835
X-RAY DIFFRACTIONr_mcbond_other0.241.52612
X-RAY DIFFRACTIONr_mcangle_it1.571210604
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.40634839
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5074.54173
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
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 8814 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.310.5
medium thermal0.642
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 440 -
Rwork0.291 7736 -
obs--86.05 %

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