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- PDB-4p5n: Structure of CNAG_02591 from Cryptococcus neoformans -

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Basic information

Entry
Database: PDB / ID: 4p5n
TitleStructure of CNAG_02591 from Cryptococcus neoformans
ComponentsHypothetical protein CNAG_02591
KeywordsSTRUCTURAL GENOMICS / CNAG_02591 / Cryptococcus neoformans / PSI-BIOLOGY / Protein Structure Initiative / New York Structural Genomics Research Consortium / NYSGRC
Function / homologySH3 type barrels. - #1060 / Hypervirulence associated protein, TUDOR domain / Hypervirulence associated proteins TUDOR domain / SH3 type barrels. / Roll / Mainly Beta / : / Hva1_TUDOR domain-containing protein
Function and homology information
Biological speciesCryptococcus neoformans (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.49 Å
Model detailsSTRUCTURAL GENOMICS
AuthorsRamagopal, U.A. / McClelland, E.E. / Toro, R. / Casadevall, A. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: Plos Pathog. / Year: 2016
Title: A Small Protein Associated with Fungal Energy Metabolism Affects the Virulence of Cryptococcus neoformans in Mammals.
Authors: McClelland, E.E. / Ramagopal, U.A. / Rivera, J. / Cox, J. / Nakouzi, A. / Prabu, M.M. / Almo, S.C. / Casadevall, A.
History
DepositionMar 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2016Group: Database references
Revision 1.2Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein CNAG_02591
B: Hypothetical protein CNAG_02591
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,28017
Polymers16,7282
Non-polymers1,55115
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-129 kcal/mol
Surface area8700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.775, 34.686, 38.253
Angle α, β, γ (deg.)73.930, 72.850, 79.460
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Hypothetical protein CNAG_02591


Mass: 8364.197 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptococcus neoformans (fungus) / Strain: H99 / Gene: CNAG_02591 / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: J9VKY2
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cd
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.3 Å3/Da / Density % sol: 46.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.2M cadmium sulfate, 2.2M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 27, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.49→50 Å / Num. obs: 23265 / % possible obs: 95.7 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.048 / Rsym value: 0.047 / Χ2: 2.17 / Net I/av σ(I): 34.382 / Net I/σ(I): 18.8 / Num. measured all: 64741
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.49-1.522.70.1479.8811411.33591.6
1.52-1.542.80.14611141.40894.2
1.54-1.572.90.12511861.44595.4
1.57-1.612.80.11511321.51894.9
1.61-1.642.90.10511671.57195.3
1.64-1.682.80.10111471.64194.9
1.68-1.722.90.09511461.89595.6
1.72-1.772.80.0812071.82895.7
1.77-1.822.80.07711722.02696.2
1.82-1.882.80.06811322.0295.7
1.88-1.942.80.06311852.31996.9
1.94-2.022.80.05411812.27896.3
2.02-2.112.80.05311712.51296.6
2.11-2.232.80.04911692.63897.2
2.23-2.372.80.0511702.75296.9
2.37-2.552.70.04611802.73497.3
2.55-2.82.70.04311882.79897.2
2.8-3.212.70.0411902.83297
3.21-4.042.60.03811673.03897
4.04-502.60.03711203.05291.9

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.7.0032refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.49→35.51 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / WRfactor Rfree: 0.1864 / WRfactor Rwork: 0.1406 / FOM work R set: 0.9174 / SU B: 1.904 / SU ML: 0.034 / SU R Cruickshank DPI: 0.0172 / SU Rfree: 0.0148 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.017 / ESU R Free: 0.015 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1802 1191 5.1 %RANDOM
Rwork0.1371 22074 --
obs0.1392 23265 95.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 116.63 Å2 / Biso mean: 16.481 Å2 / Biso min: 4.08 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å2-2.78 Å20.52 Å2
2--1.37 Å21.14 Å2
3----0.95 Å2
Refinement stepCycle: final / Resolution: 1.49→35.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1134 0 50 156 1340
Biso mean--30.5 25.03 -
Num. residues----148
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191249
X-RAY DIFFRACTIONr_angle_refined_deg1.3021.9861698
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0435160
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.21727.58658
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.07715227
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.593152
X-RAY DIFFRACTIONr_chiral_restr0.090.2194
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021928
X-RAY DIFFRACTIONr_mcbond_it1.5991.264621
X-RAY DIFFRACTIONr_mcangle_it2.0181.903778
X-RAY DIFFRACTIONr_scbond_it2.4821.67628
X-RAY DIFFRACTIONr_rigid_bond_restr14.1531249
X-RAY DIFFRACTIONr_sphericity_free43.027535
X-RAY DIFFRACTIONr_sphericity_bonded13.15751364
LS refinement shellResolution: 1.49→1.53 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.21 71 -
Rwork0.117 1580 -
all-1651 -
obs--91.57 %

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