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- PDB-5umq: Crystal structure of TnmS1, an antibiotic binding protein from St... -

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Basic information

Entry
Database: PDB / ID: 5umq
TitleCrystal structure of TnmS1, an antibiotic binding protein from Streptomyces sp. CB03234
ComponentsGlyoxalase/bleomycin resisance protein/dioxygenase
KeywordsTiancimycin-binding protein / glyoxalase/bleomycin resistance protein/dioxygenase superfamily / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Enzyme Discovery for Natural Product Biosynthesis / NatPro
Function / homology
Function and homology information


dioxygenase activity
Similarity search - Function
2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Roll / Alpha Beta
Similarity search - Domain/homology
Glyoxalase/bleomycin resisance protein/dioxygenase
Similarity search - Component
Biological speciesStreptomyces sp. CB03234 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsChang, C.Y. / Chang, C. / Nocek, B. / Rudolf, J.D. / Joachimiak, A. / Phillips Jr., G.N. / Shen, B. / Enzyme Discovery for Natural Product Biosynthesis (NatPro) / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Cell Chem Biol / Year: 2018
Title: Resistance to Enediyne Antitumor Antibiotics by Sequestration.
Authors: Chang, C.Y. / Yan, X. / Crnovcic, I. / Annaval, T. / Chang, C. / Nocek, B. / Rudolf, J.D. / Yang, D. / Babnigg, G. / Joachimiak, A. / Phillips Jr., G.N. / Shen, B.
History
DepositionJan 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 3, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.3Sep 23, 2020Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: Glyoxalase/bleomycin resisance protein/dioxygenase
B: Glyoxalase/bleomycin resisance protein/dioxygenase


Theoretical massNumber of molelcules
Total (without water)32,1382
Polymers32,1382
Non-polymers00
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-23 kcal/mol
Surface area11530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.569, 66.124, 103.354
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glyoxalase/bleomycin resisance protein/dioxygenase


Mass: 16068.983 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. CB03234 (bacteria) / Gene: tnmS1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A125SA24
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O

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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: 1.94 Å3/Da / Density % sol: 36.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 50 mM ammonium sulphate, 50 mM bis-tris propane, and 30 % v/v pentaerythriol ethoxylate (15/4 EO/OH)

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 18652 / % possible obs: 98.4 % / Redundancy: 13.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.02 / Rrim(I) all: 0.074 / Net I/σ(I): 33
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.761 / Mean I/σ(I) obs: 2.4 / Num. unique all: 890 / Num. unique obs: 890 / CC1/2: 0.88 / Rpim(I) all: 0.242 / Rrim(I) all: 0.802 / % possible all: 97.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
MOLREP5.8.0155phasing
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HC5

4hc5


Resolution: 1.95→50 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.891 / SU B: 3.787 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.188 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25621 898 5.2 %RANDOM
Rwork0.19546 ---
obs0.19843 16523 91.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.311 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2--0.16 Å20 Å2
3----0.24 Å2
Refinement stepCycle: 1 / Resolution: 1.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2000 0 0 131 2131
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192048
X-RAY DIFFRACTIONr_bond_other_d0.0020.021906
X-RAY DIFFRACTIONr_angle_refined_deg1.4491.9392776
X-RAY DIFFRACTIONr_angle_other_deg0.95134378
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3775249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.14224.364110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.10715331
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9491514
X-RAY DIFFRACTIONr_chiral_restr0.0870.2299
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212363
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02499
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_it1.5832.1981002
X-RAY DIFFRACTIONr_mcbond_other1.5772.1961001
X-RAY DIFFRACTIONr_mcangle_it2.7653.2861249
X-RAY DIFFRACTIONr_mcangle_other2.7653.2891250
X-RAY DIFFRACTIONr_scbond_it1.5592.451046
X-RAY DIFFRACTIONr_scbond_other1.5572.451046
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.673.5851528
X-RAY DIFFRACTIONr_long_range_B_refined5.18126.3792189
X-RAY DIFFRACTIONr_long_range_B_other5.08526.1952162
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 43 -
Rwork0.22 617 -
obs--48.25 %

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