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- PDB-3mgz: Crystal structure of DHBPS domain of bi-functional DHBPS/GTP cycl... -

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Basic information

Entry
Database: PDB / ID: 3mgz
TitleCrystal structure of DHBPS domain of bi-functional DHBPS/GTP cyclohydrolase II from Mycobacterium tuberculosis at pH 4.0
Components3,4-dihydroxy-2-butanone 4-phosphate synthase
KeywordsLYASE / DHBPS / ribA2 / antibacterial / drug target / Ribulose-5-phosphate / riboflavin
Function / homology
Function and homology information


GTP cyclohydrolase II / 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 / GTP binding / magnesium ion binding / zinc ion binding / cytosol
Similarity search - Function
Riboflavin biosynthesis protein RibBA / GTP cyclohydrolase II, RibA / GTP cyclohydrolase II / GTP cyclohydrolase II superfamily / GTP cyclohydrolase II / 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 ...Riboflavin biosynthesis protein RibBA / GTP cyclohydrolase II, RibA / GTP cyclohydrolase II / GTP cyclohydrolase II superfamily / GTP cyclohydrolase II / 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
Riboflavin biosynthesis protein RibBA
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsSingh, M. / Kumar, P. / Karthikeyan, S.
CitationJournal: J.Struct.Biol. / Year: 2011
Title: Structural basis for pH dependent monomer-dimer transition of 3,4-dihydroxy 2-butanone-4-phosphate synthase domain from Mycobacterium tuberculosis
Authors: Singh, M. / Kumar, P. / Karthikeyan, S.
History
DepositionApr 7, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 7, 2011Group: 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

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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)22,4203
Polymers22,2281
Non-polymers1922
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.085, 66.085, 88.188
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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


Mass: 22228.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37RA / Gene: ribA2 / Plasmid: Pet28c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A5U2B7, 3,4-dihydroxy-2-butanone-4-phosphate synthase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.5 Å3/Da / Density % sol: 50.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 25% PEG 4000, 0.2M (NH4)2SO4, 0.1M Na Acetate, pH 4.0, 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: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 24, 2010 / Details: Mirrors
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.06→50 Å / Num. all: 13576 / Num. obs: 13576 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 33.5 Å2 / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 33.9
Reflection shellResolution: 2.06→2.13 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.179 / Mean I/σ(I) obs: 9.9 / Num. unique all: 1196 / Rsym value: 0.179 / % possible all: 88.9

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Processing

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

1g57


Resolution: 2.07→34.93 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.128 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23773 657 4.9 %RANDOM
Rwork0.1876 ---
obs0.19 12718 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.446 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20.23 Å20 Å2
2--0.46 Å20 Å2
3----0.68 Å2
Refinement stepCycle: LAST / Resolution: 2.07→34.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1385 0 10 111 1506
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221410
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5471.9771911
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1915182
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.09122.58658
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.68215228
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1411515
X-RAY DIFFRACTIONr_chiral_restr0.1140.2228
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211043
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1021.5918
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.02921462
X-RAY DIFFRACTIONr_scbond_it2.583492
X-RAY DIFFRACTIONr_scangle_it4.4774.5449
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.065→2.119 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 54 -
Rwork0.196 886 -
obs--94.66 %

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