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- PDB-2vvn: BtGH84 in complex with NH-Butylthiazoline -

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Basic information

Entry
Database: PDB / ID: 2vvn
TitleBtGH84 in complex with NH-Butylthiazoline
ComponentsO-GLCNACASE BT_4395
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE / COMPLEX / INHIBITOR / GLYCOSIDASE
Function / homology
Function and homology information


protein O-GlcNAcase / : / : / [protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine/L-threonine O-N-acetyl-alpha-D-glucosaminase activity / protein deglycosylation / 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 / Glycosyl hydrolases family 84 (GH84) domain profile. / Beta-N-acetylglucosaminidase / beta-N-acetylglucosaminidase / Chitobiase/beta-hexosaminidase domain 2-like / Chitobiase; domain 2 ...: / : / Carbohydrate binding module family 32 / Bacterial GH84, post-catalytic domain / Hyaluronidase post-catalytic domain-like / Glycosyl hydrolases family 84 (GH84) domain profile. / Beta-N-acetylglucosaminidase / beta-N-acetylglucosaminidase / Chitobiase/beta-hexosaminidase domain 2-like / Chitobiase; domain 2 / Beta-hexosaminidase, bacterial type, N-terminal / Glycosyl hydrolase family 20, domain 2 / Beta-hexosaminidase-like, domain 2 / Glycosyl hydrolase, all-beta / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
AMMONIUM ION / Chem-NHT / O-GlcNAcase BT_4395
Similarity search - Component
Biological speciesBACTEROIDES THETAIOTAOMICRON (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsHe, Y. / Davies, G.J.
CitationJournal: Nat.Chem.Biol. / Year: 2008
Title: A Potent Mechanism-Inspired O-Glcnacase Inhibitor that Blocks Phosphorylation of Tau in Vivo.
Authors: Yuzwa, S.A. / Macauley, M.S. / Heinonen, J.E. / Shan, X. / Dennis, R.J. / He, Y. / Whitworth, G.E. / Stubbs, K.A. / Mceachern, E.J. / Davies, G.J. / Vocadlo, D.J.
History
DepositionJun 10, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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 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: O-GLCNACASE BT_4395
B: O-GLCNACASE BT_4395
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,7836
Polymers169,1762
Non-polymers6074
Water20,1771120
1
A: O-GLCNACASE BT_4395
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,9464
Polymers84,5881
Non-polymers3583
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: O-GLCNACASE BT_4395
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,8362
Polymers84,5881
Non-polymers2481
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)51.511, 94.503, 99.227
Angle α, β, γ (deg.)104.53, 94.00, 102.89
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B
14A
24B

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERTYRTYR4AA4 - 12925 - 150
21SERSERTYRTYR4BB4 - 12925 - 150
12TYRTYRASNASN4AA129 - 459150 - 480
22TYRTYRASNASN4BB129 - 459150 - 480
13TYRTYRHISHIS4AA460 - 593481 - 614
23TYRTYRHISHIS4BB460 - 593481 - 614
14LYSLYSLYSLYS5AA594 - 715615 - 736
24LYSLYSLYSLYS5BB594 - 715615 - 736

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein O-GLCNACASE BT_4395 / BETA-HEXOSAMINIDASE / N-ACETYL-BETA- GLUCOSAMINIDASE / BETA-N-ACETYLHEXOSAMINIDASE / HEXOSAMINIDASE ...BETA-HEXOSAMINIDASE / N-ACETYL-BETA- GLUCOSAMINIDASE / BETA-N-ACETYLHEXOSAMINIDASE / HEXOSAMINIDASE B / GH84 / BTGH84


Mass: 84587.922 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACTEROIDES THETAIOTAOMICRON (bacteria)
Strain: VPI-5482 / Plasmid: YSBLLICPET28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q89ZI2, beta-N-acetylhexosaminidase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-NH4 / AMMONIUM ION / Ammonium


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#4: Chemical ChemComp-NHT / (3AR,5R,6S,7R,7AR)-2-(ETHYLAMINO)-5-(HYDROXYMETHYL)-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D][1,3]THIAZOLE-6,7-DIOL


Mass: 248.299 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16N2O4S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1120 / 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: 2.84 Å3/Da / Density % sol: 56 % / Description: NONE
Crystal growDetails: 0.3M NH4AC, 20% GLYCEROL, 13% PEG3350, 0.1M MES PH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9804
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 8, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9804 Å / Relative weight: 1
ReflectionResolution: 1.85→76.03 Å / Num. obs: 142794 / % possible obs: 95.5 % / Observed criterion σ(I): 2 / Redundancy: 2.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.5
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2 / % possible all: 94.7

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Processing

Software
NameVersionClassification
REFMAC5.4.0065refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CHN

2chn


Resolution: 1.85→57.45 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.939 / SU B: 6.904 / SU ML: 0.105 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22424 7228 5.1 %RANDOM
Rwork0.1803 ---
obs0.18252 135522 95.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.728 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å2-0.13 Å2-0.62 Å2
2--0.35 Å2-1.79 Å2
3----0.8 Å2
Refinement stepCycle: LAST / Resolution: 1.85→57.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10517 0 39 1120 11676
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02210945
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4651.95814850
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.49751321
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.82824.842539
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.908151925
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9111552
X-RAY DIFFRACTIONr_chiral_restr0.1020.21581
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0218382
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_it0.6311.56532
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.09210596
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9634413
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.14.54237
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

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A990medium positional0.370.5
21A2663medium positional0.250.5
31A1126medium positional0.150.5
41A228medium positional0.140.5
42B224loose positional0.285
11A990medium thermal0.562
21A2663medium thermal0.712
31A1126medium thermal0.512
41A228medium thermal0.252
42B224loose thermal0.3110
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.326 555
Rwork0.288 9940
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.82780.8907-0.15933.88031.22342.42170.01430.04780.6573-0.3483-0.11120.3158-0.6393-0.30550.09680.09270.08050.01370.0275-0.09570.1393-4.411826.31476.2148
21.34470.27270.46690.67320.47581.25230.0743-0.1852-0.06270.091-0.0541-0.07010.1188-0.1255-0.0202-0.0831-0.03360.0164-0.10830.0239-0.10325.151-3.44264.6068
31.40450.51880.53771.51580.8241.59980.07290.0001-0.10750-0.15090.13830.1387-0.20580.078-0.0587-0.02590.02950.0138-0.0498-0.0873-14.3773-15.8189-22.0989
42.259-0.41130.25193.43691.16542.4632-0.0399-0.1257-0.40120.39980.02580.0640.5486-0.11980.01410.0921-0.03150.0021-0.0495-0.02160.0021-10.9567-70.48531.3859
51.0393-0.0912-0.15140.60320.29220.9836-0.00660.1330.0203-0.0774-0.0057-0.042-0.0688-0.02860.0123-0.06990.0188-0.0162-0.10510.0204-0.1084-2.1038-40.394632.0921
61.4447-0.319-0.32581.28380.49271.47340.0104-0.09640.18870.0219-0.06940.1079-0.181-0.15390.059-0.04530.0431-0.0367-0.0109-0.0457-0.08-21.4078-27.776258.8157
76.0622-2.7375-0.48233.6974-0.69463.5859-0.1031-0.5007-0.75350.04990.18290.23360.04860.0793-0.0798-0.11770.01920.0106-0.10640.1060.07546.2739-34.2374-18.8281
86.97571.76390.04472.30040.00512.8027-0.03590.5591.0933-0.14770.05090.0407-0.0144-0.0432-0.015-0.08790.0128-0.0555-0.1340.13880.2208-1.027-8.821355.5092
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 128
2X-RAY DIFFRACTION2A129 - 459
3X-RAY DIFFRACTION3A460 - 593
4X-RAY DIFFRACTION4B4 - 128
5X-RAY DIFFRACTION5B129 - 459
6X-RAY DIFFRACTION6B460 - 593
7X-RAY DIFFRACTION7A594 - 715
8X-RAY DIFFRACTION8B594 - 715

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