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- PDB-4ur9: Structure of ligand bound glycosylhydrolase -

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Basic information

Entry
Database: PDB / ID: 4ur9
TitleStructure of ligand bound glycosylhydrolase
ComponentsO-GLCNACASE BT_4395
KeywordsHYDROLASE
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
4-ethoxyquinazoline / Chem-OAN / O-GlcNAcase BT_4395
Similarity search - Component
Biological speciesBACTEROIDES THETAIOTAOMICRON (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.2 Å
AuthorsDarby, J.F. / Landstroem, J. / Roth, C. / He, Y. / Schultz, M. / Davies, G.J. / Hubbard, R.E.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2014
Title: Discovery of Selective Small-Molecule Activators of a Bacterial Glycoside Hydrolase.
Authors: Darby, J.F. / Landstrom, J. / Roth, C. / He, Y. / Davies, G.J. / Hubbard, R.E.
History
DepositionJun 27, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 2.0Oct 23, 2019Group: Atomic model / Data collection / Other / Category: atom_site / pdbx_database_status
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_sf
Revision 2.1May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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.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_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.

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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)165,7277
Polymers164,6322
Non-polymers1,0955
Water7,296405
1
A: O-GLCNACASE BT_4395
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,8443
Polymers82,3161
Non-polymers5282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: O-GLCNACASE BT_4395
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,8844
Polymers82,3161
Non-polymers5683
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.486, 162.735, 223.179
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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


Mass: 82316.109 Da / Num. of mol.: 2 / Fragment: RESIDUES 22-737
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACTEROIDES THETAIOTAOMICRON (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q89ZI2, protein O-GlcNAcase
#2: Chemical ChemComp-BK9 / 4-ethoxyquinazoline


Mass: 174.199 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H10N2O
#3: Chemical ChemComp-OAN / O-(2-ACETAMIDO-2-DEOXY D-GLUCOPYRANOSYLIDENE) AMINO-N-PHENYLCARBAMATE / PUGNAc


Mass: 353.327 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H19N3O7 / Comment: inhibitor*YM
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 405 / 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: 2.8 Å3/Da / Density % sol: 55.6 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97625
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 130125 / % possible obs: 99.5 % / Observed criterion σ(I): 0.84 / Redundancy: 6.7 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 8.7
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 0.84 / % possible all: 96.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.9_1692)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.2→48.786 Å / SU ML: 0.36 / σ(F): 1.27 / Phase error: 31.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.252 9154 5 %
Rwork0.2215 --
obs0.2231 96246 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→48.786 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10977 0 77 405 11459
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411326
X-RAY DIFFRACTIONf_angle_d0.77415334
X-RAY DIFFRACTIONf_dihedral_angle_d12.4224248
X-RAY DIFFRACTIONf_chiral_restr0.0311632
X-RAY DIFFRACTIONf_plane_restr0.0041977
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1999-2.22490.43842560.39625810X-RAY DIFFRACTION98
2.2249-2.25110.47422890.39135716X-RAY DIFFRACTION98
2.2511-2.27850.37433030.37335738X-RAY DIFFRACTION99
2.2785-2.30740.38013050.34955813X-RAY DIFFRACTION100
2.3074-2.33770.38172850.34025876X-RAY DIFFRACTION99
2.3377-2.36980.38563290.33085667X-RAY DIFFRACTION99
2.3698-2.40360.3263220.32615791X-RAY DIFFRACTION100
2.4036-2.43950.33983370.32125864X-RAY DIFFRACTION100
2.4395-2.47760.34692740.31215758X-RAY DIFFRACTION99
2.4776-2.51820.29762980.29325777X-RAY DIFFRACTION100
2.5182-2.56170.29612610.28445886X-RAY DIFFRACTION100
2.5617-2.60820.36662660.28565806X-RAY DIFFRACTION99
2.6082-2.65840.29292970.26845814X-RAY DIFFRACTION100
2.6584-2.71270.26852460.2695948X-RAY DIFFRACTION99
2.7127-2.77160.31792930.24775681X-RAY DIFFRACTION100
2.7716-2.83610.26193090.23625892X-RAY DIFFRACTION100
2.8361-2.9070.29173050.24195762X-RAY DIFFRACTION100
2.907-2.98560.27663400.23045782X-RAY DIFFRACTION100
2.9856-3.07350.24833260.22385803X-RAY DIFFRACTION100
3.0735-3.17260.28442710.22835828X-RAY DIFFRACTION100
3.1726-3.2860.25573290.22495763X-RAY DIFFRACTION99
3.286-3.41750.29093330.20945844X-RAY DIFFRACTION100
3.4175-3.5730.24763090.1945743X-RAY DIFFRACTION100
3.573-3.76140.19593150.19255807X-RAY DIFFRACTION100
3.7614-3.99690.20053170.18285854X-RAY DIFFRACTION100
3.9969-4.30530.19943510.17145770X-RAY DIFFRACTION100
4.3053-4.73830.19682970.15715810X-RAY DIFFRACTION100
4.7383-5.42320.19673510.16425733X-RAY DIFFRACTION100
5.4232-6.82960.24913420.19645818X-RAY DIFFRACTION100
6.8296-48.79820.18852980.18175785X-RAY DIFFRACTION99
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.4802-0.42680.43742.0160.35092.4935-0.28850.718-0.445-0.7920.51640.1540.5949-0.5676-0.18530.6294-0.3991-0.03431.1025-0.07060.373617.232625.9154220.0331
21.49870.3914-0.43660.7171-0.38712.2747-0.01150.10290.06010.00530.12440.0305-0.1228-0.2757-0.09680.1390.0217-0.01240.60120.08360.18524.85545.4538243.0157
31.0842-0.4778-0.61311.58711.26934.01860.0125-0.12030.03930.2626-0.03130.12410.1308-0.65230.10870.20490.003-0.03470.60280.17870.2138.920634.6883271.1189
44.7760.194-1.23570.3926-0.16770.68460.1211-0.25830.52410.22760.03590.0165-0.3665-0.5766-0.19590.36090.12360.01230.63990.0360.254611.911847.287274.2696
55.45820.3273-0.45863.3131-1.45320.677-0.0153-0.73680.39290.2494-0.18060.1261-1.1684-0.48190.19831.00830.2653-0.22770.5206-0.08920.38426.257657.0213282.249
69.5917-2.1437-2.1248.838-2.31636.0293-0.0716-0.25830.90110.38020.1776-0.6311-1.41130.8488-0.09270.7648-0.0768-0.28310.372-0.00240.494331.691857.3311280.5444
72.5299-0.6181-0.56335.91032.37640.9887-0.0704-0.4284-0.00540.1218-0.07160.1158-0.1494-0.01410.20110.3088-0.07130.00670.62960.00880.026312.944330.1616316.4106
82.79720.58090.69775.23512.19575.7433-0.0221-0.3520.23660.0952-0.00880.0924-0.39320.06230.03780.1487-0.01080.01770.5226-0.06450.161918.142328.0236318.7027
94.061-0.50630.06182.3037-0.20791.8888-0.0546-0.1822-0.25720.0531-0.0334-0.2850.23570.31760.08230.1939-0.0043-0.00840.410.00590.215438.88469.4311300.408
104.3280.21441.04263.5987-2.84236.7473-0.1124-0.0669-0.7692-0.1458-0.1-0.27370.7325-0.28480.15850.2733-0.02480.08140.2789-0.03990.3225.2851-3.8841299.9903
111.2362-0.17640.09290.5135-0.24341.3381-0.06650.305-0.0759-0.11220.19510.19940.2105-0.6363-0.10140.2114-0.1591-0.02220.53430.0150.19418.672814.4872288.5169
121.1370.07721.22571.61090.61281.4636-0.16220.43890.1214-0.4080.1180.13250.1768-0.8065-0.02570.3139-0.2465-0.00110.80950.10910.2268.628219.5947267.6352
133.6878-2.0823.27021.5067-1.47843.5770.39320.6963-0.4167-0.3204-0.01730.15450.6771-0.1325-0.42820.439-0.2101-0.01970.6594-0.05620.22938.35079.458269.1566
146.8406-1.96340.77373.1280.17721.96030.18890.65160.1366-0.5172-0.1206-0.16440.8643-0.0865-0.0860.9236-0.15040.02290.8037-0.05090.268620.04713.9585255.8872
157.3232-1.25523.58382.91160.23896.85120.13590.34650.3733-0.74840.0776-0.8471.09050.7245-0.22210.980.08140.18810.82470.07930.545630.5641-0.6488252.6643
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 5 THROUGH 128 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 129 THROUGH 488 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 489 THROUGH 544 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 545 THROUGH 616 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 617 THROUGH 667 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 668 THROUGH 716 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 3 THROUGH 34 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 35 THROUGH 128 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 129 THROUGH 278 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 279 THROUGH 348 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 349 THROUGH 488 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 489 THROUGH 544 )
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 545 THROUGH 579 )
14X-RAY DIFFRACTION14CHAIN 'B' AND (RESID 580 THROUGH 662 )
15X-RAY DIFFRACTION15CHAIN 'B' AND (RESID 663 THROUGH 716 )

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