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- PDB-5awv: Crystal structure of glycopeptide hexose oxidase DBV29 complexed ... -

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Basic information

Entry
Database: PDB / ID: 5awv
TitleCrystal structure of glycopeptide hexose oxidase DBV29 complexed with teicoplanin
Components
  • Putative hexose oxidase
  • TEICOPLANIN
KeywordsOXIDOREDUCTASE/ANTIBIOTIC / Oxidoreductase-antibiotic complex
Function / homology
Function and homology information


acyltransferase activity / glycosyltransferase activity / monooxygenase activity / FAD binding
Similarity search - Function
Vanillyl-alcohol Oxidase; Chain A, domain 3 - #20 / Berberine/berberine-like / Berberine and berberine like / Vanillyl-alcohol Oxidase; Chain A, domain 3 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 / FAD linked oxidase, N-terminal / FAD binding domain / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. ...Vanillyl-alcohol Oxidase; Chain A, domain 3 - #20 / Berberine/berberine-like / Berberine and berberine like / Vanillyl-alcohol Oxidase; Chain A, domain 3 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 / FAD linked oxidase, N-terminal / FAD binding domain / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
teicoplanin / CITRIC ACID / FLAVIN-ADENINE DINUCLEOTIDE / alpha-D-mannopyranose / 2-amino-2-deoxy-beta-D-glucopyranuronic acid / 8-METHYLNONANOIC ACID / Putative hexose oxidase
Similarity search - Component
Biological speciesNonomuraea sp. ATCC 39727 (bacteria)
ACTINOPLANES TEICHOMYCETICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsLiu, Y.C. / Li, T.L.
Funding support Taiwan, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology96-2628-B-001-026-MY3 Taiwan
Ministry of Science and Technology98-2311-B-001-014-MY3 Taiwan
CitationJournal: Nat. Chem. Biol. / Year: 2011
Title: Interception of teicoplanin oxidation intermediates yields new antimicrobial scaffolds.
Authors: Liu, Y.C. / Li, Y.S. / Lyu, S.Y. / Hsu, L.J. / Chen, Y.H. / Huang, Y.T. / Chan, H.C. / Huang, C.J. / Chen, G.H. / Chou, C.C. / Tsai, M.D. / Li, T.L.
History
DepositionJul 9, 2015Deposition site: PDBJ / Processing site: PDBJ
SupersessionAug 19, 2015ID: 4K3T
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_poly / entity_src_gen / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_alt_source_flag / _pdbx_entity_nonpoly.name / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _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: Putative hexose oxidase
B: Putative hexose oxidase
C: Putative hexose oxidase
D: Putative hexose oxidase
I: TEICOPLANIN
J: TEICOPLANIN
K: TEICOPLANIN
L: TEICOPLANIN
M: TEICOPLANIN
N: TEICOPLANIN
O: TEICOPLANIN
P: TEICOPLANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,39849
Polymers237,89212
Non-polymers9,50637
Water25,2211400
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.791, 150.778, 124.853
Angle α, β, γ (deg.)90.00, 98.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Protein/peptide , 2 types, 12 molecules ABCDIJKLMNOP

#1: Protein
Putative hexose oxidase


Mass: 57059.012 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nonomuraea sp. ATCC 39727 (bacteria) / Gene: dbv29 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7WZ62
#2: Protein/peptide
TEICOPLANIN


Type: Glycopeptide / Class: Antibiotic, Antimicrobial / Mass: 1206.984 Da / Num. of mol.: 8 / Source method: obtained synthetically / Source: (synth.) ACTINOPLANES TEICHOMYCETICUS (bacteria) / References: teicoplanin

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Sugars , 3 types, 22 molecules

#6: Sugar
ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking, Glycopeptide / Class: Antibiotic, Antimicrobial / Mass: 180.156 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H12O6 / References: teicoplanin
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#7: 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.: 8 / Source method: obtained synthetically / Formula: C8H15NO6 / References: teicoplanin
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
#8: Sugar
ChemComp-N1L / 2-amino-2-deoxy-beta-D-glucopyranuronic acid / 2-amino-2-deoxy-beta-D-glucuronic acid / 2-amino-2-deoxy-D-glucuronic acid / 2-amino-2-deoxy-glucuronic acid


Type: D-saccharide, beta linking, Glycopeptide / Class: Antibiotic, Antimicrobial / Mass: 193.155 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C6H11NO6 / References: teicoplanin
IdentifierTypeProgram
b-D-GlcpANIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 1415 molecules

#3: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H8O7
#5: Chemical
ChemComp-T55 / 8-METHYLNONANOIC ACID


Type: Glycopeptide / Class: Antibiotic, Antimicrobial / Mass: 172.265 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H20O2 / References: teicoplanin
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1400 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 17% PEG 3350, 0.2M diammonium hydrogen citrate, pH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.93→29.51 Å / Num. obs: 163843 / % possible obs: 97.8 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 14.97
Reflection shellResolution: 1.93→1.96 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.573 / Mean I/σ(I) obs: 2.87 / % possible all: 97.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WDW

2wdw


Resolution: 1.93→29.4 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.696 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20464 8214 5 %RANDOM
Rwork0.15594 ---
obs0.15842 155630 97.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.621 Å2
Baniso -1Baniso -2Baniso -3
1--2.12 Å20 Å2-1.06 Å2
2---0.04 Å20 Å2
3---2.37 Å2
Refinement stepCycle: 1 / Resolution: 1.93→29.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16104 0 615 1400 18119
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0217285
X-RAY DIFFRACTIONr_bond_other_d0.0040.0215494
X-RAY DIFFRACTIONr_angle_refined_deg2.1622.04123721
X-RAY DIFFRACTIONr_angle_other_deg1.2523.01535671
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.76151988
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.72623.26724
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.113152380
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.99415124
X-RAY DIFFRACTIONr_chiral_restr0.1340.22502
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02119295
X-RAY DIFFRACTIONr_gen_planes_other0.0030.023940
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_it2.8392.8367994
X-RAY DIFFRACTIONr_mcbond_other2.8222.8337986
X-RAY DIFFRACTIONr_mcangle_it3.9564.239964
X-RAY DIFFRACTIONr_mcangle_other3.9564.239964
X-RAY DIFFRACTIONr_scbond_it4.2453.679291
X-RAY DIFFRACTIONr_scbond_other4.2453.679292
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.4075.36613758
X-RAY DIFFRACTIONr_long_range_B_refined9.13527.95421503
X-RAY DIFFRACTIONr_long_range_B_other9.13527.95621504
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.935→1.985 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 606 -
Rwork0.229 11036 -
obs--94.02 %

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