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- PDB-2aq6: X-ray crystal structure of mycobacterium tuberculosis pyridoxine ... -

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Basic information

Entry
Database: PDB / ID: 2aq6
TitleX-ray crystal structure of mycobacterium tuberculosis pyridoxine 5'-phosphate oxidase complexed with pyridoxal 5'-phosphate at 1.7 a resolution
ComponentsPYRIDOXINE 5'-PHOSPHATE OXIDASE
KeywordsOXIDOREDUCTASE / PYRIDOXINE 5'-PHOSPHATE OXIDASE / PYRIDOXAL 5'-PHOSPHATE / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


vitamin B6 metabolic process / coenzyme F420 binding / oxidoreductase activity, acting on the CH-CH group of donors / Oxidoreductases / pyridoxal phosphate binding / FMN binding / protein homodimerization activity / cytosol
Similarity search - Function
F420-binding domain, putative / Pyridoxamine 5'-phosphate oxidase, putative / Pyridoxamine 5'-phosphate oxidase / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll / Mainly Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / F420H(2)-dependent reductase Rv1155
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsBiswal, B.K. / Cherney, M.M. / Wang, M. / Garen, C. / James, M.N. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Structures of Mycobacterium tuberculosispyridoxine 5'-phosphate oxidase and its complexes with flavin mononucleotide and pyridoxal 5'-phosphate.
Authors: Biswal, B.K. / Cherney, M.M. / Wang, M. / Garen, C. / James, M.N.
History
DepositionAug 17, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 14, 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: PYRIDOXINE 5'-PHOSPHATE OXIDASE
B: PYRIDOXINE 5'-PHOSPHATE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8903
Polymers32,6432
Non-polymers2471
Water6,828379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-5 kcal/mol
Surface area13840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.87, 55.35, 54.52
Angle α, β, γ (deg.)90.0, 107.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PYRIDOXINE 5'-PHOSPHATE OXIDASE


Mass: 16321.480 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: RV1155 / Plasmid: PET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O06553
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 379 / 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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 12% PEG 8000, 8% ethylene glycol, 30 mM KF, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1158 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 31, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 1.7→37.87 Å / Num. all: 29370 / Num. obs: 28603 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 12.1 Å2 / Rsym value: 0.066
Reflection shellResolution: 1.7→1.76 Å / % possible all: 90.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
Blu-Icedata collection
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→37.87 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1415107.38 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.194 1390 4.9 %RANDOM
Rwork0.191 ---
obs0.191 28603 97.5 %-
all-29370 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 64.4727 Å2 / ksol: 0.387703 e/Å3
Displacement parametersBiso mean: 16.3 Å2
Baniso -1Baniso -2Baniso -3
1--1.72 Å20 Å2-0.83 Å2
2---0.52 Å20 Å2
3---2.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.7→37.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2232 0 16 379 2627
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_improper_angle_d0.83
LS refinement shellHighest resolution: 1.7 Å / Total num. of bins used: 6 /
Num. reflection% reflection
Rwork4213 -
Rfree-4.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4plp.parplp.top

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