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- PDB-5njo: Roll out the beta-barrel: structure and mechanism of Pac13, a uni... -

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Basic information

Entry
Database: PDB / ID: 5njo
TitleRoll out the beta-barrel: structure and mechanism of Pac13, a unique nucleoside dehydratase
ComponentsPutative cupin_2 domain-containing isomerase
KeywordsSTRUCTURAL PROTEIN / Pac13 Cupin Pacidamycin
Function / homologyRmlC-like cupin domain superfamily / isomerase activity / RmlC-like jelly roll fold / Putative cupin_2 domain-containing isomerase
Function and homology information
Biological speciesStreptomyces coeruleorubidus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsMichailidou, F. / Bent, A.F. / Naismith, J.H. / Goss, R.J.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research Council United Kingdom
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
DepositionMar 29, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Putative cupin_2 domain-containing isomerase


Theoretical massNumber of molelcules
Total (without water)13,8291
Polymers13,8291
Non-polymers00
Water3,261181
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.490, 66.490, 54.710
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-251-

HOH

21A-308-

HOH

31A-380-

HOH

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Components

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


Mass: 13829.337 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 BL21(DE3) (bacteria) / Variant (production host): RIPL / References: UniProt: E2EKP5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.52 Å3/Da / Density % sol: 51.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.8 / Details: 0.1 M Tris pH 8.8, 20% w/v PEG8K, 0.2 M MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9797 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 1.55→57.58 Å / Num. obs: 20630 / % possible obs: 100 % / Redundancy: 10.9 % / Biso Wilson estimate: 18.63 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 23.5
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.776 / Num. unique obs: 2031 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
xia2data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NJN

5njn


Resolution: 1.55→57.58 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.393 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.077 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20115 1056 5.1 %RANDOM
Rwork0.17994 ---
obs0.18099 19574 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.958 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20.08 Å20 Å2
2--0.16 Å20 Å2
3----0.5 Å2
Refinement stepCycle: 1 / Resolution: 1.55→57.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms976 0 0 181 1157
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0191002
X-RAY DIFFRACTIONr_bond_other_d0.0010.02902
X-RAY DIFFRACTIONr_angle_refined_deg1.2721.9281361
X-RAY DIFFRACTIONr_angle_other_deg0.70932071
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9485120
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.48123.26952
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.32815154
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.57157
X-RAY DIFFRACTIONr_chiral_restr0.080.2147
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211143
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02252
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_it0.9911.863483
X-RAY DIFFRACTIONr_mcbond_other0.9881.862482
X-RAY DIFFRACTIONr_mcangle_it1.6252.79602
X-RAY DIFFRACTIONr_mcangle_other1.6242.791603
X-RAY DIFFRACTIONr_scbond_it1.7652.153519
X-RAY DIFFRACTIONr_scbond_other1.7632.153520
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8723.122760
X-RAY DIFFRACTIONr_long_range_B_refined8.23418.3421218
X-RAY DIFFRACTIONr_long_range_B_other6.67716.5211124
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.551→1.591 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 77 -
Rwork0.24 1425 -
obs--99.87 %

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