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- PDB-2x7p: The Conserved Candida albicans CA3427 Gene Product Defines a New ... -

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Basic information

Entry
Database: PDB / ID: 2x7p
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 / homology
Function and homology information


cellular response to sulfate starvation / fungal biofilm matrix / periplasmic space
Similarity search - Function
: / Ca3427-like PBP / NMT1/THI5 like / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / 2-(2-ETHOXYETHOXY)ETHANOL / CARBON DIOXIDE / Ca3427-like PBP 2 domain-containing protein
Similarity search - Component
Biological speciesCANDIDA ALBICANS (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.34 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 16, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / 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.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 / _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)37,10912
Polymers36,3711
Non-polymers73811
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.588, 66.849, 113.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 7 types, 151 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-AE3 / 2-(2-ETHOXYETHOXY)ETHANOL


Mass: 134.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O3
#6: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H4O2
#7: Chemical ChemComp-CO2 / CARBON DIOXIDE


Mass: 44.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.44 Å3/Da / Density % sol: 49.52 % / Description: NONE
Crystal growDetails: 21 % PEG8000, CALCIUM ACETATE 0.2 M, TRIS 0.1 M, 30 % GLYCEROL PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979774, 0.979958
DetectorType: MARRESEARCH / Date: Jul 3, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9797741
20.9799581
ReflectionResolution: 2.34→23.88 Å / Num. obs: 13442 / % possible obs: 99.1 % / Observed criterion σ(I): 10 / Redundancy: 5.5 % / Biso Wilson estimate: 24.14 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 4.1
Reflection shellResolution: 2.34→2.47 Å / Redundancy: 3 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 3 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.34→23.88 Å / SU ML: 0.28 / σ(F): 2.46 / Phase error: 21.89 / Stereochemistry target values: ML
Details: DISORDERED SIDE CHAIN ARE MODELED WITH A OCCUPANCY LESS THAN 1 WITHOUT ALTERNATE CONFORMATION.
RfactorNum. reflection% reflection
Rfree0.256 674 5 %
Rwork0.209 --
obs0.211 13441 94.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.03 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 22.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.0613 Å20 Å20 Å2
2--0.7268 Å20 Å2
3----0.7881 Å2
Refinement stepCycle: LAST / Resolution: 2.34→23.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2434 0 46 140 2620
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0012553
X-RAY DIFFRACTIONf_angle_d0.3853457
X-RAY DIFFRACTIONf_dihedral_angle_d11.217916
X-RAY DIFFRACTIONf_chiral_restr0.03387
X-RAY DIFFRACTIONf_plane_restr0.001446
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3413-2.52190.29061160.22692024X-RAY DIFFRACTION77
2.5219-2.77530.30181300.2312561X-RAY DIFFRACTION96
2.7753-3.17610.27071540.21752633X-RAY DIFFRACTION98
3.1761-3.99850.23961320.18342711X-RAY DIFFRACTION99
3.9985-23.87660.22091420.19582838X-RAY DIFFRACTION99

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