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- PDB-3ls6: Crystal structure of 3,4-Dihydroxy-2-butanone 4-phosphate synthas... -

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Basic information

Entry
Database: PDB / ID: 3ls6
TitleCrystal structure of 3,4-Dihydroxy-2-butanone 4-phosphate synthase in complex with sulfate and zinc
Components3,4-Dihydroxy-2-butanone 4-phosphate synthase
KeywordsLYASE / DHBPS / DIMETAL CENTER / DRUG TARGET / antibacterial / Magnesium / 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 / 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
3,4-dihydroxy-2-butanone 4-phosphate synthase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.86 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 12, 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 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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 / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_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: 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)47,79518
Polymers46,6712
Non-polymers1,12416
Water6,035335
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-24 kcal/mol
Surface area15590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.276, 77.161, 146.827
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-305-

ZN

21B-483-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 351 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: 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
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 335 / 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: 2.01 Å3/Da / Density % sol: 38.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% PEG 5000 MME, 100mM MES Sodium Salt, 200mM Ammonium sulfate, pH 6.5, VAPOR DIFFUSION, SITTING 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: Oct 30, 2009 / Details: OSMIC VARIMAX
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.86→73.41 Å / Num. all: 31811 / Num. obs: 31811 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 20.34 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 29.2
Reflection shellResolution: 1.86→1.92 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.192 / Mean I/σ(I) obs: 9.32 / Num. unique all: 3140 / Rsym value: 0.185 / % possible all: 99.7

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
CCP4model building
REFMAC5.5.0070refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G57

1g57


Resolution: 1.86→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.354 / SU ML: 0.073 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19662 1614 5.1 %RANDOM
Rwork0.15919 ---
all0.16104 31811 --
obs0.16104 31803 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.347 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20 Å20 Å2
2---0.57 Å20 Å2
3---0.17 Å2
Refine analyzeLuzzati coordinate error obs: 0.138 Å
Refinement stepCycle: LAST / Resolution: 1.86→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3041 0 33 335 3409
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223142
X-RAY DIFFRACTIONr_angle_refined_deg1.3221.9724273
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3695422
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.42724.015137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.53615524
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3781528
X-RAY DIFFRACTIONr_chiral_restr0.090.2506
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212369
X-RAY DIFFRACTIONr_mcbond_it0.6961.52038
X-RAY DIFFRACTIONr_mcangle_it1.29823284
X-RAY DIFFRACTIONr_scbond_it2.29431104
X-RAY DIFFRACTIONr_scangle_it4.0374.5981
LS refinement shellResolution: 1.86→1.908 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 103 -
Rwork0.215 2231 -
obs--99.4 %

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