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

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Basic information

Entry
Database: PDB / ID: 5njn
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 / SAD / Resolution: 1.6 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 2.0Nov 6, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Structure summary
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _atom_site.occupancy / _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


Theoretical massNumber of molelcules
Total (without water)13,9701
Polymers13,9701
Non-polymers00
Water1,892105
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.800, 66.800, 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-221-

HOH

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Components

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


Mass: 13970.023 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


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 51.24 %
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: 0.97945 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: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.6→57.85 Å / Num. obs: 19005 / % possible obs: 100 % / Redundancy: 31.5 % / Biso Wilson estimate: 14.75 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 32.7
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 29.8 % / Rmerge(I) obs: 0.741 / Mean I/σ(I) obs: 6.2 / Num. unique obs: 1384 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
xia2data reduction
SCALAdata scaling
PHENIX1.9.1692phasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→57.85 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.321 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.082 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20659 979 5.2 %RANDOM
Rwork0.18448 ---
obs0.18555 18000 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 17.674 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0.02 Å20 Å2
2---0.05 Å20 Å2
3---0.15 Å2
Refinement stepCycle: 1 / Resolution: 1.6→57.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms968 0 0 105 1073
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.019994
X-RAY DIFFRACTIONr_bond_other_d0.0030.02867
X-RAY DIFFRACTIONr_angle_refined_deg1.2951.9341351
X-RAY DIFFRACTIONr_angle_other_deg0.86832007
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.675119
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.15823.26952
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.47515145
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.677157
X-RAY DIFFRACTIONr_chiral_restr0.0810.2146
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211118
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02225
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_it0.7131.628479
X-RAY DIFFRACTIONr_mcbond_other0.7041.627478
X-RAY DIFFRACTIONr_mcangle_it1.192.439597
X-RAY DIFFRACTIONr_mcangle_other1.1912.439598
X-RAY DIFFRACTIONr_scbond_it1.2761.828515
X-RAY DIFFRACTIONr_scbond_other1.2751.828516
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.042.673755
X-RAY DIFFRACTIONr_long_range_B_refined4.00119.7221044
X-RAY DIFFRACTIONr_long_range_B_other3.79819.3031029
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 91 -
Rwork0.224 1285 -
obs--100 %

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