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- PDB-2x9l: Crystal structure of deacetylase-bog complex in biosynthesis path... -

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Basic information

Entry
Database: PDB / ID: 2x9l
TitleCrystal structure of deacetylase-bog complex in biosynthesis pathway of teicoplanin.
ComponentsN-ACYL GLM PEUDO-TEICOPLANIN DEACETYLASE
KeywordsHYDROLASE
Function / homology
Function and homology information


glycoside metabolic process / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / acyltransferase activity / ligase activity / glycosyltransferase activity / metal ion binding
Similarity search - Function
LmbE-like / N-acetylglucosaminyl phosphatidylinositol deacetylase-related / Putative deacetylase LmbE-like domain superfamily / GlcNAc-PI de-N-acetylase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
LmbE family N-acetylglucosaminyl deacetylase
Similarity search - Component
Biological speciesACTINOPLANES TEICHOMYCETICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.732 Å
AuthorsChan, H.C. / Huang, Y.T. / Lyu, S.Y. / Huang, C.J. / Li, Y.S. / Liu, Y.C. / Chou, C.C. / Tsai, M.D. / Li, T.L.
CitationJournal: Mol.Biosyst. / Year: 2011
Title: Regioselective Deacetylation Based on Teicoplanin-Complexed Orf2 Crystal Structures.
Authors: Chan, H.C. / Huang, Y.T. / Lyu, S.Y. / Huang, C.J. / Li, Y.S. / Liu, Y.C. / Chou, C.C. / Tsai, M.D. / Li, T.L.
History
DepositionMar 23, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Database references / Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _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.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.pdbx_leaving_atom_flag / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-ACYL GLM PEUDO-TEICOPLANIN DEACETYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6533
Polymers30,2951
Non-polymers3582
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.452, 64.028, 50.342
Angle α, β, γ (deg.)90.00, 99.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein N-ACYL GLM PEUDO-TEICOPLANIN DEACETYLASE / PUTATIVE UNCHARACTERIZED PROTEIN TCP14 / TEICOPLANIN PSEUDOAGLYCONE DEACETYLASE ORF2


Mass: 30295.033 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: BOG
Source: (gene. exp.) ACTINOPLANES TEICHOMYCETICUS (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6ZZJ1
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.6 % / Description: NONE
Crystal growpH: 8 / Details: pH 8

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.96
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 1.73→27.03 Å / Num. obs: 25339 / % possible obs: 91.3 % / Observed criterion σ(I): 3 / Redundancy: 2.7 % / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 21.5
Reflection shellResolution: 1.7→50 Å

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Processing

Software
NameClassification
SOLVEphasing
RESOLVEphasing
PHENIXrefinement
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1.732→27.031 Å / SU ML: 0.22 / σ(F): 1.35 / Phase error: 21.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2172 1258 5 %
Rwork0.1857 --
obs0.1873 25339 91.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.866 Å2 / ksol: 0.361 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.0188 Å20 Å2-0.3945 Å2
2---0.3108 Å20 Å2
3---0.3296 Å2
Refinement stepCycle: LAST / Resolution: 1.732→27.031 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1992 0 21 253 2266
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062060
X-RAY DIFFRACTIONf_angle_d1.0452803
X-RAY DIFFRACTIONf_dihedral_angle_d19.327757
X-RAY DIFFRACTIONf_chiral_restr0.066308
X-RAY DIFFRACTIONf_plane_restr0.004372
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7319-1.80130.29181330.22362242X-RAY DIFFRACTION78
1.8013-1.88320.24111230.20872716X-RAY DIFFRACTION93
1.8832-1.98250.23571280.19392767X-RAY DIFFRACTION94
1.9825-2.10660.25231530.18462742X-RAY DIFFRACTION94
2.1066-2.26920.21361280.17392743X-RAY DIFFRACTION93
2.2692-2.49740.21451470.17922744X-RAY DIFFRACTION93
2.4974-2.85850.21411540.18772709X-RAY DIFFRACTION93
2.8585-3.60.19421560.17942687X-RAY DIFFRACTION92
3.6-27.03420.20391360.17962731X-RAY DIFFRACTION91

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