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- PDB-5oo5: Streptomyces PAC13 with uridine uronic acid -

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Basic information

Entry
Database: PDB / ID: 5oo5
TitleStreptomyces PAC13 with uridine uronic acid
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 uronic acid / 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 5, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)14,3702
Polymers14,1121
Non-polymers2581
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.489, 66.489, 55.232
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-333-

HOH

21A-504-

HOH

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Components

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


Mass: 14111.614 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coeruleorubidus (bacteria)
Gene: pac13, pacM / Production host: Escherichia coli (E. coli) / References: UniProt: E2EKP5
#2: Chemical ChemComp-UUA / uridine uronic acid


Mass: 258.185 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H10N2O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 51.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.8 / Details: 16% PEG3350,0.1M MgCl2,0.2MBis-Tris pH 8.8

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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: Jun 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→57.85 Å / Num. obs: 13723 / % possible obs: 99.3 % / Redundancy: 3.7 % / Biso Wilson estimate: 16.66 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 19.4
Reflection shellResolution: 1.78→1.93 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 5 / Num. unique obs: 2788 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→57.58 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.359 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.112 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19512 673 4.9 %RANDOM
Rwork0.15311 ---
obs0.15508 12994 98.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.655 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20.03 Å20 Å2
2--0.06 Å2-0 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.78→57.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms977 0 18 208 1203
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0191116
X-RAY DIFFRACTIONr_bond_other_d0.0010.02980
X-RAY DIFFRACTIONr_angle_refined_deg1.2221.9461533
X-RAY DIFFRACTIONr_angle_other_deg0.70932262
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.9615140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.87523.3959
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.26415172
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.275159
X-RAY DIFFRACTIONr_chiral_restr0.0830.2161
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211339
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02288
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_it0.921.865533
X-RAY DIFFRACTIONr_mcbond_other0.9171.863532
X-RAY DIFFRACTIONr_mcangle_it1.5354.182682
X-RAY DIFFRACTIONr_mcangle_other1.5354.183683
X-RAY DIFFRACTIONr_scbond_it1.572.147583
X-RAY DIFFRACTIONr_scbond_other1.5692.147583
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6444.663851
X-RAY DIFFRACTIONr_long_range_B_refined5.9319.8371358
X-RAY DIFFRACTIONr_long_range_B_other5.3999.0921257
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.783→1.829 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 63 -
Rwork0.2 914 -
obs--98.29 %

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