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- PDB-4jna: Crystal structure of the DepH complex with dimethyl-FK228 -

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Basic information

Entry
Database: PDB / ID: 4jna
TitleCrystal structure of the DepH complex with dimethyl-FK228
Components
  • DepH
  • Dimethyl FK228
KeywordsOxidoreductase/Oxidoreductase inhibitor / disulfide bond formation / FK228 / depsipeptide / FAD-dependent oxidoreductase / Oxidoreductase-Oxidoreductase inhibitor complex
Function / homology
Function and homology information


thioredoxin-disulfide reductase (NADPH) activity / cell redox homeostasis / nucleotide binding
Similarity search - Function
FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
Dimethyl FK228 / FLAVIN-ADENINE DINUCLEOTIDE / PHOSPHATE ION / DepH
Similarity search - Component
Biological speciesChromobacterium violaceum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsLi, J. / Wang, C. / Zhang, Z.M. / Zhou, J.H. / Cheng, E.
CitationJournal: Sci Rep / Year: 2014
Title: The structural basis of an NADP+-independent dithiol oxidase in FK228 biosynthesis.
Authors: Li, J. / Wang, C. / Zhang, Z.M. / Cheng, Y.Q. / Zhou, J.
History
DepositionMar 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_validate_polymer_linkage / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr1_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DepH
B: DepH
H: Dimethyl FK228
I: Dimethyl FK228
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,75814
Polymers74,6814
Non-polymers2,07710
Water4,792266
1
A: DepH
I: Dimethyl FK228
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3807
Polymers37,3402
Non-polymers1,0405
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-30 kcal/mol
Surface area13430 Å2
MethodPISA
2
B: DepH
H: Dimethyl FK228
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3777
Polymers37,3402
Non-polymers1,0375
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-27 kcal/mol
Surface area13770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.283, 154.283, 71.828
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Detailsbiological unit is the same as asym.

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABHI

#1: Protein DepH


Mass: 36751.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromobacterium violaceum (bacteria) / Strain: No. 968 / Gene: depH / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A4ZPY8
#2: Protein/peptide Dimethyl FK228


Type: Cyclic depsipeptide / Class: Antibiotic / Mass: 588.780 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: DIMETHYL FK228 IS THE REDUCED AND MODIFIED FORM OF ROMIDEPSIN. THE DISULFIDE INTRAMOLECULAR LINKAGE OF ROMIDEPSIN IS BROKEN, AND BOTH SULFHYDRYL GROUPS ARE METHYLATED.
References: Dimethyl FK228

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Non-polymers , 6 types, 276 molecules

#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 266 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsROMIDEPSIN (INN, TRADE NAME ISTODAX), CODENAMED FK228 AND FR901228, IS A NATURAL PRODUCT OBTAINED ...ROMIDEPSIN (INN, TRADE NAME ISTODAX), CODENAMED FK228 AND FR901228, IS A NATURAL PRODUCT OBTAINED FROM THE BACTERIA CHROMOBACTERIUM VIOLACEUM, AND WORKS BY BLOCKING ENZYMES KNOWN AS HISTONE DEACETYLASES AND INDUCING APOPTOSIS. DIMETHYL FK228 IS THE REDUCED AND MODIFIED FORM OF ROMIDEPSIN, WHICH DOES NOT HAVE THE DISULFIDE INTRAMOLECULAR LINKAGE, AND BOTH SULFHYDRYL GROUPS ARE METHYLATED.

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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: 2.86 Å3/Da / Density % sol: 57.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1 M citric acid, 0.2M (NH4)2SO4, 11.75 % PEG4000, pH 5.0, microseeding, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97877 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Oct 26, 2011
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97877 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 57606 / % possible obs: 97.1 % / Redundancy: 9.8 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 12.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2-2.077.40.625190.9
2.07-2.159.50.52199.7
2.15-2.259.10.425191.5
2.25-2.379.40.262190.7
2.37-2.5210.30.1671100
2.52-2.7110.50.1171100
2.71-2.9910.70.0841100
2.99-3.4210.70.071100
3.42-4.3110.20.085199.5
4.31-5010.20.042198.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3FBS

3fbs


Resolution: 2→33.981 Å / SU ML: 0.25 / σ(F): 1.33 / Phase error: 22.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2216 2886 5.07 %
Rwork0.1519 --
obs0.1555 56898 96.56 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→33.981 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4532 0 135 266 4933
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064837
X-RAY DIFFRACTIONf_angle_d1.226563
X-RAY DIFFRACTIONf_dihedral_angle_d19.2851822
X-RAY DIFFRACTIONf_chiral_restr0.093703
X-RAY DIFFRACTIONf_plane_restr0.004862
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.03280.32281370.24812283X-RAY DIFFRACTION88
2.0328-2.06790.28761350.21712451X-RAY DIFFRACTION94
2.0679-2.10550.28841260.17252638X-RAY DIFFRACTION99
2.1055-2.1460.27021430.16152616X-RAY DIFFRACTION100
2.146-2.18980.28161180.19882648X-RAY DIFFRACTION100
2.1898-2.23740.41411160.28772022X-RAY DIFFRACTION77
2.2374-2.28940.58641220.42331901X-RAY DIFFRACTION73
2.2894-2.34660.25211430.17612634X-RAY DIFFRACTION100
2.3466-2.41010.19631270.13172654X-RAY DIFFRACTION100
2.4101-2.4810.21311430.13182636X-RAY DIFFRACTION100
2.481-2.5610.22441570.13622621X-RAY DIFFRACTION100
2.561-2.65250.24271340.13442661X-RAY DIFFRACTION100
2.6525-2.75870.24781470.14132649X-RAY DIFFRACTION100
2.7587-2.88420.24431330.14262673X-RAY DIFFRACTION100
2.8842-3.03610.24121380.15022664X-RAY DIFFRACTION100
3.0361-3.22620.17371500.13942660X-RAY DIFFRACTION100
3.2262-3.47510.20861400.14442675X-RAY DIFFRACTION100
3.4751-3.82440.22061540.14542649X-RAY DIFFRACTION99
3.8244-4.37680.15591490.12182708X-RAY DIFFRACTION100
4.3768-5.51050.17211560.11282734X-RAY DIFFRACTION100
5.5105-33.98620.17841180.15192835X-RAY DIFFRACTION97

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