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- PDB-2y3r: Structure of the tirandamycin-bound FAD-dependent tirandamycin ox... -

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Basic information

Entry
Database: PDB / ID: 2y3r
TitleStructure of the tirandamycin-bound FAD-dependent tirandamycin oxidase TamL in P21 space group
ComponentsTAML
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


FAD binding / oxidoreductase activity / metal ion binding
Similarity search - Function
Vanillyl-alcohol Oxidase; Chain A, domain 3 - #20 / Oxygen oxidoreductase covalent FAD-binding site / Berberine/berberine-like / Berberine and berberine like / Oxygen oxidoreductases covalent FAD-binding site. / 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 ...Vanillyl-alcohol Oxidase; Chain A, domain 3 - #20 / Oxygen oxidoreductase covalent FAD-binding site / Berberine/berberine-like / Berberine and berberine like / Oxygen oxidoreductases covalent FAD-binding site. / 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
FLAVIN-ADENINE DINUCLEOTIDE / TIRANDAMYCIN E / TIRANDAMYCIN D / TamL
Similarity search - Component
Biological speciesSTREPTOMYCES SP. 307-9 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsCarlson, J.C. / Li, S. / Gunatilleke, S.S. / Anzai, Y. / Burr, D.A. / Podust, L.M. / Sherman, D.H.
CitationJournal: Nat.Chem / Year: 2011
Title: Tirandamycin Biosynthesis is Mediated by Co-Dependent Oxidative Enzymes
Authors: Carlson, J.C. / Li, S. / Gunatilleke, S.S. / Anzai, Y. / Burr, D.A. / Podust, L.M. / Sherman, D.H.
History
DepositionDec 22, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2011Group: Database references / Non-polymer description / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Dec 20, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TAML
B: TAML
C: TAML
D: TAML
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,46529
Polymers232,7594
Non-polymers5,70725
Water36,0302000
1
A: TAML
B: TAML
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,15113
Polymers116,3792
Non-polymers2,77211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7690 Å2
ΔGint-76.1 kcal/mol
Surface area33380 Å2
MethodPISA
2
C: TAML
D: TAML
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,31416
Polymers116,3792
Non-polymers2,93514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8170 Å2
ΔGint-95.5 kcal/mol
Surface area33300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.088, 106.171, 151.172
Angle α, β, γ (deg.)90.00, 94.63, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 4 / Auth seq-ID: 5 - 495 / Label seq-ID: 35 - 525

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

NCS oper:
IDCodeMatrixVector
1given(-0.9999, 0.001807, -0.01266), (-0.002332, -0.9991, 0.04157), (-0.01257, 0.0416, 0.9991)24.13, -1.718, 0.258
2given(-1, 1.7E-5, 0.00371), (-8.0E-5, 0.9997, -0.02611), (-0.003709, -0.02611, -0.9997)29.33, 17.44, 75.06
3given(1, 0.003254, 0.001702), (0.003283, -0.9998, -0.01723), (0.001646, 0.01724, -0.9999)-6.078, -16.05, 75.67

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
TAML


Mass: 58189.711 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: COVALENT LINK BETWEEN 8ALPHA METHYL GROUP OF FAD TO N1 OF HIS 62 COVALENT LINK BETWEEN C6 ATOM OF FAD AND CYS 122
Source: (gene. exp.) STREPTOMYCES SP. 307-9 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODON PLUS RP / References: UniProt: D3Y1I2

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Non-polymers , 7 types, 2025 molecules

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


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-TIR / TIRANDAMYCIN E


Mass: 403.469 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H29NO6
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-TRK / TIRANDAMYCIN D


Mass: 401.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H27NO6
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2000 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsFLAVIN ADENINE DINUCLEOTIDE (FAD): COVALENT LINK BETWEEN 8ALPHA METHYL GROUP OF FAD TO N-1 OF HIS62. ...FLAVIN ADENINE DINUCLEOTIDE (FAD): COVALENT LINK BETWEEN 8ALPHA METHYL GROUP OF FAD TO N-1 OF HIS62. COVALENT LINK BETWEEN C-6 ATOM OF FAD AND CYS122 TIRANDAMYCIN E (TIR): TAML SUBSTRATE TIRANDAMYCIN D (TRK): PRODUCT OF THE TAML-CATALYZED REACTION MAGNESIUM ION (MG): CHELATED BY THE TIRANDAMYCIN AND TWO WATER MOLECULES
Sequence detailsHIS8-TAG AND TEV PROTEASE SITE ARE ENGINEERED AT THE N- TERMINUS.

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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: 2.63 Å3/Da / Density % sol: 53.3 % / Description: NONE
Crystal growTemperature: 296 K / pH: 7
Details: 9% PEG 4000, 0.2 M MGCL, 23 DEGREES CELSIUS., pH 7.0

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 20, 2010 / Details: MIRRORS
RadiationMonochromator: SI (111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 1.79→19.82 Å / Num. obs: 161395 / % possible obs: 76.7 % / Observed criterion σ(I): 1.5 / Redundancy: 2.9 % / Biso Wilson estimate: 18.8 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.6
Reflection shellResolution: 1.79→1.89 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 2.4 / % possible all: 26.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Y08

2y08


Resolution: 1.79→150.68 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.937 / SU B: 5.953 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 204-208 AND 364-368 ARE POORLY ORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.219 8138 5.1 %RANDOM
Rwork0.14603 ---
obs0.14969 152628 76.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.683 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20 Å2
2---0.17 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.79→150.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14985 0 380 2000 17365
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.02116208
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.021.96722249
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.20352038
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.34422.039721
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.884152262
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.21915174
X-RAY DIFFRACTIONr_chiral_restr0.140.22383
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02112806
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_it1.6441.59995
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.545216059
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.09936213
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.0574.56190
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.43316208
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 3375 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.210.5
2Bmedium positional0.20.5
3Cmedium positional0.220.5
4Dmedium positional0.160.5
1Amedium thermal1.372
2Bmedium thermal1.412
3Cmedium thermal1.52
4Dmedium thermal1.382
LS refinement shellResolution: 1.79→1.837 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 179 -
Rwork0.288 3317 -
obs--22.59 %

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