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- PDB-2riu: Alternative models for two crystal structures of Candida albicans... -

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Basic information

Entry
Database: PDB / ID: 2riu
TitleAlternative models for two crystal structures of Candida albicans 3,4-dihydroxy-2-butanone 4-phosphate synthase- alternate interpreation
Components3,4-dihydroxy-2-butanone 4-phosphate synthase
KeywordsISOMERASE / alternate model / Magnesium / Manganese / Metal-binding / Riboflavin biosynthesis
Function / homology
Function and homology information


3,4-dihydroxy-2-butanone-4-phosphate synthase / 3,4-dihydroxy-2-butanone-4-phosphate synthase activity / riboflavin biosynthetic process / mitochondrial intermembrane space / metal ion binding / cytosol
Similarity search - Function
3,4-dihydroxy-2-butanone 4-phosphate synthase, RibB / 3,4-dihydroxy-2-butanone 4-phosphate synthase / DHBP synthase / DHBP synthase RibB-like alpha/beta domain superfamily / DHBP synthase / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
RIBULOSE-5-PHOSPHATE / 3,4-dihydroxy-2-butanone 4-phosphate synthase
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsStenkamp, R.E. / Le Trong, I.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Alternative models for two crystal structures of Candida albicans 3,4-dihydroxy-2-butanone 4-phosphate synthase.
Authors: Le Trong, I. / Stenkamp, R.E.
#1: Journal: J.Mol.Biol. / Year: 2004
Title: Potential anti-infective targets in pathogenic yeasts: structure and properties of 3,4-dihydroxy-2-butanone 4-phosphate synthase of Candida albicans.
Authors: Echt, S. / Bauer, S. / Steinbacher, S. / Huber, R. / Bacher, A. / Fischer, M.
History
DepositionOct 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: 3,4-dihydroxy-2-butanone 4-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9152
Polymers22,6851
Non-polymers2301
Water2,720151
1
A: 3,4-dihydroxy-2-butanone 4-phosphate synthase
hetero molecules

A: 3,4-dihydroxy-2-butanone 4-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8304
Polymers45,3702
Non-polymers4602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area3250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.597, 47.900, 40.200
Angle α, β, γ (deg.)90.000, 70.620, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein 3,4-dihydroxy-2-butanone 4-phosphate synthase / DHBP synthase


Mass: 22684.982 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (yeast) / Gene: RIB3 / Plasmid: pnco-carib3-syn / Production host: Escherichia coli (E. coli) / Strain (production host): xl1 / References: UniProt: Q5A3V6
#2: Sugar ChemComp-5RP / RIBULOSE-5-PHOSPHATE


Type: saccharide / Mass: 230.110 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H11O8P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.19 Å3/Da / Density % sol: 43.94 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.542 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 3, 2003
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.66→51.71 Å / Num. obs: 20361

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3data extraction
RefinementResolution: 1.7→51.71 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.927 / SU B: 1.734 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.215 1050 5.2 %RANDOM
Rwork0.185 ---
obs0.187 20361 93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.836 Å2
Baniso -1Baniso -2Baniso -3
1--0.85 Å20 Å20.33 Å2
2--0.85 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.7→51.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1521 0 14 151 1686
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221553
X-RAY DIFFRACTIONr_angle_refined_deg1.1291.9982098
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4125192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.6324.71470
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.90415284
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.0661511
X-RAY DIFFRACTIONr_chiral_restr0.0750.2241
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021153
X-RAY DIFFRACTIONr_nbd_refined0.2070.2792
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21083
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.2140
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1240.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2110.227
X-RAY DIFFRACTIONr_mcbond_it0.4681.5996
X-RAY DIFFRACTIONr_mcangle_it0.76421558
X-RAY DIFFRACTIONr_scbond_it1.4483611
X-RAY DIFFRACTIONr_scangle_it2.3984.5540
LS refinement shellResolution: 1.7→1.741 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 72 -
Rwork0.23 1328 -
all-1400 -
obs--87.55 %

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