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- PDB-5oo8: Streptomyces PAC13 (H42Q) with uridine -

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Basic information

Entry
Database: PDB / ID: 5oo8
TitleStreptomyces PAC13 (H42Q) with uridine
ComponentsPutative cupin_2 domain-containing isomerase
KeywordsBIOSYNTHETIC PROTEIN / Pac13 / Dehydratase / Pacidamycin
Function / homologyRmlC-like cupin domain superfamily / isomerase activity / RmlC-like jelly roll fold / URIDINE / Putative cupin_2 domain-containing isomerase
Function and homology information
Biological speciesStreptomyces coeruleorubidus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsChung, C. / Michailidou, F.
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2017
Title: Pac13 is a Small, Monomeric Dehydratase that Mediates the Formation of the 3'-Deoxy Nucleoside of Pacidamycins.
Authors: Michailidou, F. / Chung, C.W. / Brown, M.J.B. / Bent, A.F. / Naismith, J.H. / Leavens, W.J. / Lynn, S.M. / Sharma, S.V. / Goss, R.J.M.
History
DepositionAug 6, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Oct 11, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative cupin_2 domain-containing isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4083
Polymers14,1021
Non-polymers3062
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area680 Å2
ΔGint1 kcal/mol
Surface area6610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.390, 66.390, 54.841
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-339-

HOH

21A-438-

HOH

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Components

#1: Protein Putative cupin_2 domain-containing isomerase / Putative uncharacterized protein pac13


Mass: 14101.596 Da / Num. of mol.: 1 / Mutation: H42Q
Source method: isolated from a genetically manipulated source
Details: H42Q mutation from native sequence
Source: (gene. exp.) Streptomyces coeruleorubidus (bacteria)
Gene: pac13, pacM / Production host: Escherichia coli (E. coli) / References: UniProt: E2EKP5
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-URI / URIDINE


Mass: 244.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12N2O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.55 Å3/Da / Density % sol: 51.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.2 M potassium sodium tartrate, 20 % w/v PEG-335

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Feb 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.78→57.5 Å / Num. obs: 13630 / % possible obs: 99.5 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 19.2
Reflection shellResolution: 1.78→1.92 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 2778 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→57.5 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.536 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.107 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19407 672 5 %RANDOM
Rwork0.1654 ---
obs0.16673 12900 99.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.196 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å2-0.12 Å20 Å2
2---0.24 Å2-0 Å2
3---0.77 Å2
Refinement stepCycle: LAST / Resolution: 1.78→57.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms968 0 21 141 1130
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0191070
X-RAY DIFFRACTIONr_bond_other_d0.0010.02948
X-RAY DIFFRACTIONr_angle_refined_deg1.1251.9251462
X-RAY DIFFRACTIONr_angle_other_deg0.67332186
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8475131
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.30823.57156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.69315163
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.099158
X-RAY DIFFRACTIONr_chiral_restr0.070.2156
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021252
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02270
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_it1.0162.48509
X-RAY DIFFRACTIONr_mcbond_other1.0062.478508
X-RAY DIFFRACTIONr_mcangle_it1.6645.567645
X-RAY DIFFRACTIONr_mcangle_other1.6665.57646
X-RAY DIFFRACTIONr_scbond_it1.8482.869561
X-RAY DIFFRACTIONr_scbond_other1.8482.868561
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.166.248818
X-RAY DIFFRACTIONr_long_range_B_refined5.91612.4871199
X-RAY DIFFRACTIONr_long_range_B_other5.91312.4881200
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.782→1.828 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 64 -
Rwork0.251 936 -
obs--98.72 %

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