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- PDB-2xad: Crystal structure of deacetylase-teicoplanin complex in biosynthe... -

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Basic information

Entry
Database: PDB / ID: 2xad
TitleCrystal structure of deacetylase-teicoplanin complex in biosynthesis pathway of teicoplanin
Components
  • N-ACYL GLM PEUDO-TEICOPLANIN DEACETYLASE
  • TEICOPLANIN
KeywordsOXIDOREDUCTASE/ANTIBIOTIC / OXIDOREDUCTASE-ANTIBIOTIC COMPLEX / ANTIBIOTIC / A40926 / GLYCOPEPTIDE
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
Teicoplanin A2-2 beta-D-Glucopyranuronic acid / beta-D-mannopyranose / 2-amino-2-deoxy-beta-D-glucopyranose / 8-METHYLNONANOIC ACID / LmbE family N-acetylglucosaminyl deacetylase
Similarity search - Component
Biological speciesACTINOPLANES TEICHOMYCETICUS (bacteria)
NONOMURAEA SP. ATCC 39727 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 31, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2012Group: Other
Revision 1.2Jan 15, 2014Group: Database references / Other / Version format compliance
Revision 2.0Apr 24, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Polymer sequence
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / entity_poly / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.recvd_author_approval ..._entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_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 2.2Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-ACYL GLM PEUDO-TEICOPLANIN DEACETYLASE
B: N-ACYL GLM PEUDO-TEICOPLANIN DEACETYLASE
C: N-ACYL GLM PEUDO-TEICOPLANIN DEACETYLASE
D: N-ACYL GLM PEUDO-TEICOPLANIN DEACETYLASE
E: TEICOPLANIN
F: TEICOPLANIN
G: TEICOPLANIN
H: TEICOPLANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,92324
Polymers125,9128
Non-polymers3,01116
Water14,664814
1
A: N-ACYL GLM PEUDO-TEICOPLANIN DEACETYLASE
E: TEICOPLANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2316
Polymers31,4782
Non-polymers7534
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-7.5 kcal/mol
Surface area15020 Å2
MethodPISA
2
B: N-ACYL GLM PEUDO-TEICOPLANIN DEACETYLASE
F: TEICOPLANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2316
Polymers31,4782
Non-polymers7534
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-7.8 kcal/mol
Surface area14860 Å2
MethodPISA
3
C: N-ACYL GLM PEUDO-TEICOPLANIN DEACETYLASE
G: TEICOPLANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2316
Polymers31,4782
Non-polymers7534
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-10.6 kcal/mol
Surface area14880 Å2
MethodPISA
4
D: N-ACYL GLM PEUDO-TEICOPLANIN DEACETYLASE
H: TEICOPLANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2316
Polymers31,4782
Non-polymers7534
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-5.2 kcal/mol
Surface area14810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.775, 70.713, 76.313
Angle α, β, γ (deg.)113.89, 108.29, 98.20
Int Tables number1
Space group name H-MP1

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Components

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Protein / Protein/peptide , 2 types, 8 molecules ABCDEFGH

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


Mass: 30270.990 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ACTINOPLANES TEICHOMYCETICUS (bacteria)
Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q6ZZJ1
#2: Protein/peptide
TEICOPLANIN


Type: Glycopeptide / Class: Antibiotic, Antimicrobial / Mass: 1206.984 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) NONOMURAEA SP. ATCC 39727 (bacteria) / References: Teicoplanin A2-2 beta-D-Glucopyranuronic acid

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Sugars , 3 types, 12 molecules

#3: Sugar
ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose


Type: D-saccharide, beta linking, Glycopeptide / Class: Antibiotic, Antimicrobial / Mass: 180.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / References: Teicoplanin A2-2 beta-D-Glucopyranuronic acid
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking, Glycopeptide / Class: Antibiotic, Antimicrobial / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / References: Teicoplanin A2-2 beta-D-Glucopyranuronic acid
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Sugar
ChemComp-GCS / 2-amino-2-deoxy-beta-D-glucopyranose / beta-D-glucosamine / 2-amino-2-deoxy-beta-D-glucose / 2-amino-2-deoxy-D-glucose / 2-amino-2-deoxy-glucose / D-GLUCOSAMINE


Type: D-saccharide, beta linking, Glycopeptide / Class: Antibiotic, Antimicrobial / Mass: 179.171 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H13NO5 / References: Teicoplanin A2-2 beta-D-Glucopyranuronic acid
IdentifierTypeProgram
DGlcpNbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 818 molecules

#6: Chemical
ChemComp-T55 / 8-METHYLNONANOIC ACID


Type: Glycopeptide / Class: Antibiotic, Antimicrobial / Mass: 172.265 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H20O2 / References: Teicoplanin A2-2 beta-D-Glucopyranuronic acid
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 814 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, HIS 164 TO ASN ENGINEERED RESIDUE IN CHAIN B, HIS 164 TO ASN ...ENGINEERED RESIDUE IN CHAIN A, HIS 164 TO ASN ENGINEERED RESIDUE IN CHAIN B, HIS 164 TO ASN ENGINEERED RESIDUE IN CHAIN C, HIS 164 TO ASN ENGINEERED RESIDUE IN CHAIN D, HIS 164 TO ASN TEICPLANIN IS A FAMILY OF TETRACYCLIC GLYCOPEPTIDE ANTIBIOTICS. THE SCAFFOLD IS A HEPTAPEPTIDE FURTHER GLYCOSYLATED BY THREE MONO SACCHARIDES: MANNOSE, N-ACETYLGLUCOSAMINE AND BETA-D-GLUCOSAMINE AND ONLY DIFFER BY THE SIDE CHAIN ATTACHED TO THE LATTER. HERE, TEICPLANIN IS REPRESENTED BY GROUPING TOGETHER THE SEQUENCE (SEQRES) AND 4 LIGANDS (HET). GROUP: 1 NAME: TEICPLANIN CHAIN: E, F, G, H COMPONENT_1: PEPTIDE LIKE SEQUENCE RESIDUES 701 TO 707 COMPONENT_2: SUGAR RESIDUES 708, 709 AND 710 COMPONENT_3: FATTY ACID RESIDUE 711 DESCRIPTION: TEICPLANIN IS A TETRACYCLIC HEPTAPEPTIDE GLYCOSYLATED BY THREE MONOSCCARIDES, RESIDUES 708, 709 AND 710, ON RESIDUES 707, 706 AND 704, RESPECTIVELY. THE FATTY ACID IS LINKED TO THE BETA-D-GLUCOSAMINE (RESIDUE 710)
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: 43.64 % / Description: NONE

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.96
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 101452 / % possible obs: 95.8 % / Observed criterion σ(I): 3 / Redundancy: 4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 36.14
Reflection shellHighest resolution: 1.7 Å / % possible all: 95

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Processing

SoftwareName: REFMAC / Version: 5.5.0109 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.928 / SU B: 2.306 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2368 5379 5 %RANDOM
Rwork0.20075 ---
obs0.20256 101452 95.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.089 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å20.07 Å2-0.06 Å2
2--0.7 Å20.55 Å2
3---0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8377 0 188 814 9379
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0218816
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3222.01812068
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2851022
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.75923.286420
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.397151253
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0651577
X-RAY DIFFRACTIONr_chiral_restr0.1550.21316
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0216925
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_it1.4891.55164
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.42328280
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.73733652
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.5694.53788
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: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 383 -
Rwork0.25 7381 -
obs--94.11 %

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