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- PDB-1k4l: Crystal Structure of 3,4-dihydroxy-2-butanone 4-phosphate synthas... -

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Basic information

Entry
Database: PDB / ID: 1k4l
TitleCrystal Structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase in complex with two Manganese ions
Components3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase
KeywordsISOMERASE / dihydroxybutanone phosphate synthase / riboflavin biosynthesis / antimicrobial target / structure-based design
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
: / 3,4-dihydroxy-2-butanone 4-phosphate synthase
Similarity search - Component
Biological speciesMagnaporthe grisea (fungus)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.6 Å
AuthorsLiao, D.-I. / Zheng, Y.-J. / Viitanen, P.V. / Jordan, D.B.
CitationJournal: Biochemistry / Year: 2002
Title: Structural definition of the active site and catalytic mechanism of 3,4-dihydroxy-2-butanone-4-phosphate synthase.
Authors: Liao, D.I. / Zheng, Y.J. / Viitanen, P.V. / Jordan, D.B.
History
DepositionOct 8, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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.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.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

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)25,3385
Polymers25,0361
Non-polymers3024
Water3,765209
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)50,67710
Polymers50,0732
Non-polymers6048
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area5640 Å2
ΔGint-114 kcal/mol
Surface area15980 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)53.366, 88.346, 43.747
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-1169-

HOH

DetailsThe biological assembly is a homodimer. Applying the following symmetry related operation on the coordinates of the monomer in the asymmetric unit would generate the 2nd half of the dimer. rotation matrix -1.00000 0.00000 0.00000 0.00000 -1.00000 0.00000 0.00000 0.00000 1.00000 translation -1, -1, 0

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Components

#1: Protein 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase


Mass: 25036.338 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnaporthe grisea (fungus) / Gene: rice blast fungi / Plasmid: PET-24a(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q8TG90, Isomerases; Intramolecular transferases; Transferring other groups
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.06 Å3/Da / Density % sol: 40.24 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Li2SO4, MES-NaOH, PEG5000 Monomethyl ether, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Details: Liao, D.-I., (2000) Acta Crystallogr, D56, 1495. / PH range low: 6.5 / PH range high: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
17 mg/mlprotein1drop
224-30 %PEG5000 MME1reservoir
30.2 M1reservoirLi2SO4
40.1 MMES-NaOH1reservoirpH6.0-6.5

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 18, 2000 / Details: MSC focusing mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. all: 26458 / Num. obs: 26458 / % possible obs: 94.3 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 21.5
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 3 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2 / Num. unique all: 969 / % possible all: 70.6
Reflection
*PLUS
Num. measured all: 106303 / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 70.6 %

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Processing

Software
NameClassification
TNTrefinement
DENZOdata reduction
SCALEPACKdata scaling
TNTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1K49 but with no waters.

1k49


Resolution: 1.6→15 Å / σ(F): 2
RfactorNum. reflection
Rfree0.267 2614
Rwork0.199 -
all-26412
obs-25979
Refinement stepCycle: LAST / Resolution: 1.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1631 0 12 209 1852
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg2.5
X-RAY DIFFRACTIONt_bond_d0.015
Refinement
*PLUS
Highest resolution: 1.6 Å / σ(F): 2 / Rfactor obs: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: t_angle_deg / Dev ideal: 2.5

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