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- PDB-3lqu: Crystal structure of 3,4-Dihydroxy-2-butanone 4-phosphate synthas... -

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Basic information

Entry
Database: PDB / ID: 3lqu
TitleCrystal structure of 3,4-Dihydroxy-2-butanone 4-phosphate synthase complexed with Ribulose-5 phosphate
Components3,4-dihydroxy-2-butanone 4-phosphate synthase
KeywordsLYASE / DHBPS / R5P / ribB / Metal binding / Riboflavin biosynthesis
Function / homology
Function and homology information


GTP cyclohydrolase II activity / 3,4-dihydroxy-2-butanone-4-phosphate synthase / 3,4-dihydroxy-2-butanone-4-phosphate synthase activity / riboflavin biosynthetic process / manganese ion binding / magnesium ion binding / cytosol
Similarity search - Function
DHBP synthase / 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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
5-O-phosphono-D-xylulose / 3,4-dihydroxy-2-butanone 4-phosphate synthase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.522 Å
AuthorsKumar, P. / Karthikeyan, S.
CitationJournal: Proteins / Year: 2010
Title: Potential anti-bacterial drug target: structural characterization of 3,4-dihydroxy-2-butanone-4-phosphate synthase from Salmonella typhimurium LT2.
Authors: Kumar, P. / Singh, M. / Gautam, R. / Karthikeyan, S.
History
DepositionFeb 10, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 5, 2014Group: Database references
Revision 1.3Nov 1, 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 / 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
B: 3,4-dihydroxy-2-butanone 4-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9013
Polymers46,6712
Non-polymers2301
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-25 kcal/mol
Surface area15330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.236, 77.386, 149.372
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-364-

HOH

21B-393-

HOH

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Components

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


Mass: 23335.439 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: ribB, STM3195 / Plasmid: pET28c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P66032, 3,4-dihydroxy-2-butanone-4-phosphate synthase
#2: Sugar ChemComp-5SP / 5-O-phosphono-D-xylulose / D-xylulose 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.: 128 / 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: 2.05 Å3/Da / Density % sol: 40.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% PEG 8000, 100mM MES-Na, 0.2M Ammonium Salt, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.542 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 18, 2009 / Details: Osmic VariMax
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.52→50 Å / Num. all: 12300 / Num. obs: 12279 / % possible obs: 92.3 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Biso Wilson estimate: 29.6 Å2 / Rmerge(I) obs: 0.147 / Rsym value: 0.147 / Net I/σ(I): 7.85
Reflection shellResolution: 2.52→2.61 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 2.01 / Num. unique all: 1112 / Rsym value: 0.487 / % possible all: 85.6

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
CCP4model building
PHENIX(phenix.refine: 1.6_289)refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G57

1g57


Resolution: 2.522→19.53 Å / SU ML: 0.41 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0.09 / Phase error: 27.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2735 555 4.85 %Random
Rwork0.1817 ---
all0.1862 12002 --
obs0.1862 11447 86.22 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.553 Å2 / ksol: 0.372 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.2649 Å20 Å20 Å2
2---13.0187 Å20 Å2
3---9.7538 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: LAST / Resolution: 2.522→19.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3005 0 14 128 3147
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073058
X-RAY DIFFRACTIONf_angle_d1.1084144
X-RAY DIFFRACTIONf_dihedral_angle_d17.9661129
X-RAY DIFFRACTIONf_chiral_restr0.069490
X-RAY DIFFRACTIONf_plane_restr0.004550
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5223-2.77550.37961220.252237676
2.7755-3.17560.31421510.2083264785
3.1756-3.99530.25081330.1645285991
3.9953-19.53060.22831490.1552301092

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