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- PDB-5uvd: Crystal structure of an antigenic nucleotidyltransferase-like pro... -

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Basic information

Entry
Database: PDB / ID: 5uvd
TitleCrystal structure of an antigenic nucleotidyltransferase-like protein from Paracoccidioides brasiliensis
ComponentsNucleotidyltransferase-like protein
KeywordsTRANSFERASE / antigen / putative nucleotidyltransferase
Function / homologyNucleotidyltransferase superfamily / Uncharacterized protein
Function and homology information
Biological speciesParacoccidioides brasiliensis
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.86 Å
AuthorsNagem, R.A.P. / Costa, M.A.F. / Rodrigues, F.T.G. / Coitinho, J.B.C.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Brazilian National Council for Scientific and Technological Development (CNPq)484466/2007-0 Brazil
CitationJournal: Mol.Immunol. / Year: 2019
Title: Structural and immunological characterization of a new nucleotidyltransferase-like antigen from Paracoccidioides brasiliensis.
Authors: Coitinho, J.B. / Costa, M.A.F. / Melo, E.M. / Morais, E.A. / de Andrade, L.G.A. / da Rocha, A.M. / de Magalhaes, M.T.Q. / Favaro, D.C. / Bleicher, L. / Pedroso, E.R.P. / Goes, A.M. / Nagem, R.A.P.
History
DepositionFeb 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Aug 14, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleotidyltransferase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8304
Polymers24,7571
Non-polymers733
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.649, 51.105, 121.190
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 Nucleotidyltransferase-like protein


Mass: 24757.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccidioides brasiliensis (strain Pb18) (fungus)
Strain: Pb18 / Gene: PADG_08402 / Plasmid: pET28a(TEV)
Details (production host): pET28a modified to contain TEV protease cleavage site
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C1GM11
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Description
12.141.5thin and long rod-like crystals
22.141.5thin and long rod-like crystals
Crystal grow
Temperature (K)Crystal-IDMethodDetailsPH range
293.151vapor diffusion, hanging drop0.25 M MgCl2, 25% PEG 4000, 0.1 M Tris-HCl pH 7.0 - 8,07.0 - 8.0
293.152vapor diffusion, hanging drop0.25 M MgCl2, 25% PEG 4000, 0.1 M Tris-HCl pH 7.0 - 8,0 Crystal was incubated in a cryo-soaking solution containing 100 mM NaI and 10% (v/v) ethylene glycol7.0 - 8.0

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Data collection

Diffraction
IDMean temperature (K)Ambient temp detailsCrystal-ID
1100nitrogen stream1
2100nitrogen stream2
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONLNLS W01B-MX211.4587
SYNCHROTRONLNLS W01B-MX221.4587
Detector
TypeIDDetectorDateDetails
DECTRIS PILATUS 2M1PIXELMay 24, 2013collimating mirror and toroidal bendable mirror
MAR CCD 165 mm2CCDApr 14, 2014collimating mirror and toroidal bendable mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111) double-crystal monochromatorSINGLE WAVELENGTHMx-ray1
2Si(111) double-crystal monochromatorSINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.45871
21
Reflection

Biso Wilson estimate: 22.5 Å2 / Entry-ID: 5UVD / Observed criterion σ(I): -3

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)CC1/2Rmerge(I) obsDiffraction-IDNet I/σ(I)
1.86-47.091789497.99.50.9980.088119.2
1.68-31.773975186.11.90.039218.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Diffraction-ID% possible all
1.86-1.975.50.4094.226130.954189.9
1.68-1.711.70.1723.71586268.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
PHENIX1.8.2refinement
XDSJanuary 10, 2014 BUILT=20140307data processing
DENZO2.3.2data processing
XDSJanuary 10, 2014 BUILT=20140307data scaling
HKL-20002.2.0data scaling
AutoSol1.8.2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.86→47.09 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.92 / SU B: 3.152 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.144 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22168 895 5 %RANDOM
Rwork0.15909 ---
obs0.16216 16999 97.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 17.673 Å2
Baniso -1Baniso -2Baniso -3
1--0.93 Å20 Å20 Å2
2--2.25 Å2-0 Å2
3----1.33 Å2
Refinement stepCycle: 1 / Resolution: 1.86→47.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1718 0 3 247 1968
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0191749
X-RAY DIFFRACTIONr_bond_other_d0.0060.021713
X-RAY DIFFRACTIONr_angle_refined_deg1.8781.9752372
X-RAY DIFFRACTIONr_angle_other_deg1.07533945
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2365217
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.06124.68479
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.74115316
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9541512
X-RAY DIFFRACTIONr_chiral_restr0.1110.2274
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211974
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02386
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_it1.3381.487871
X-RAY DIFFRACTIONr_mcbond_other1.3251.485870
X-RAY DIFFRACTIONr_mcangle_it1.9082.2211087
X-RAY DIFFRACTIONr_mcangle_other1.9092.2221088
X-RAY DIFFRACTIONr_scbond_it2.3081.833878
X-RAY DIFFRACTIONr_scbond_other2.3081.832878
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5782.6251285
X-RAY DIFFRACTIONr_long_range_B_refined5.57313.6122182
X-RAY DIFFRACTIONr_long_range_B_other5.23613.0412085
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.86→1.908 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 56 -
Rwork0.242 1064 -
obs--85.24 %

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