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- PDB-2x7q: The conserved Candida albicans CA3427 gene product defines a new ... -

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Basic information

Entry
Database: PDB / ID: 2x7q
TitleThe conserved Candida albicans CA3427 gene product defines a new family of proteins exhibiting the generic periplasmic binding protein structural fold
ComponentsPOSSIBLE THIAMINE BIOSYNTHESIS ENZYME
KeywordsUNKNOWN FUNCTION
Function / homologySsuA/THI5-like / NMT1/THI5 like / fungal biofilm matrix / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / metal ion binding / Alpha Beta / SsuA/THI5-like domain-containing protein
Function and homology information
Biological speciesCANDIDA ALBICANS (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSantini, S. / Monchois, V. / Mouz, N. / Rousselle, T. / Claverie, J.M. / Abergel, C.
CitationJournal: Plos One / Year: 2011
Title: The Conserved Candida Albicans Ca3427 Gene Product Defines a New Family of Proteins Exhibiting the Generic Periplasmic Binding Protein Structural Fold
Authors: Santini, S. / Claverie, J.M. / Mouz, N. / Rousselle, T. / Maza, C. / Monchois, V. / Abergel, C.
History
DepositionMar 3, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_leaving_atom_flag / _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_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_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: POSSIBLE THIAMINE BIOSYNTHESIS ENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5434
Polymers36,3711
Non-polymers1723
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.411, 65.724, 128.203
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 POSSIBLE THIAMINE BIOSYNTHESIS ENZYME / CA3427


Mass: 36371.113 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CANDIDA ALBICANS (yeast) / Strain: NIH3147 / Plasmid: PSF04, PQE80 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / References: UniProt: Q59X88
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, MET 1 TO LEU

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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: 2.62 Å3/Da / Density % sol: 53.09 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.975627
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 3, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975627 Å / Relative weight: 1
ReflectionResolution: 2→128.2 Å / Num. obs: 17895 / % possible obs: 76.7 % / Observed criterion σ(I): 10 / Redundancy: 8 % / Biso Wilson estimate: 14.78 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 6.5
Reflection shellResolution: 2→2.11 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 2.7 / % possible all: 72.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2X7P

2x7p


Resolution: 2→23.887 Å / SU ML: 0.2 / σ(F): 0.05 / Phase error: 22.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2364 935 5.1 %
Rwork0.2177 --
obs0.2186 17895 75.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 24.861 Å2 / ksol: 0.375 e/Å3
Displacement parametersBiso mean: 13.651 Å2
Baniso -1Baniso -2Baniso -3
1-0.2987 Å20 Å20 Å2
2--3.138 Å20 Å2
3----3.4366 Å2
Refinement stepCycle: LAST / Resolution: 2→23.887 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2434 0 8 220 2662
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022524
X-RAY DIFFRACTIONf_angle_d0.4783431
X-RAY DIFFRACTIONf_dihedral_angle_d14.66911
X-RAY DIFFRACTIONf_chiral_restr0.035386
X-RAY DIFFRACTIONf_plane_restr0.001442
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.10550.27621100.24942302X-RAY DIFFRACTION71
2.1055-2.23730.25911280.24452394X-RAY DIFFRACTION74
2.2373-2.40990.25381300.24392418X-RAY DIFFRACTION74
2.4099-2.65210.30731230.25032424X-RAY DIFFRACTION74
2.6521-3.03520.24211290.24532406X-RAY DIFFRACTION73
3.0352-3.82150.20911540.1912435X-RAY DIFFRACTION73
3.8215-23.88910.19651610.17863198X-RAY DIFFRACTION91

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