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- PDB-2nv0: Structure of the glutaminase subunit Pdx2 (YaaE) of PLP synthase ... -

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Basic information

Entry
Database: PDB / ID: 2nv0
TitleStructure of the glutaminase subunit Pdx2 (YaaE) of PLP synthase from Bacillus subtilis
ComponentsGlutamine amidotransferase subunit pdxT
KeywordsTRANSFERASE / 3-Layer(aba) Sandwich / Rossmann fold / Glutaminase
Function / homology
Function and homology information


pyridoxine metabolic process / glutaminase complex / pyridoxal 5'-phosphate synthase (glutamine hydrolysing) / pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity / pyridoxal phosphate biosynthetic process / L-glutamine catabolic process / glutaminase / glutaminase activity / identical protein binding / cytosol
Similarity search - Function
Pyridoxal 5'-phosphate synthase subunit PdxT/SNO / PdxT/SNO family, conserved site / SNO glutamine amidotransferase family / PdxT/SNO family family signature. / PdxT/SNO family profile. / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Pyridoxal 5'-phosphate synthase subunit PdxT
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsStrohmeier, M. / Tews, I. / Sinning, I.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Structure of a bacterial pyridoxal 5'-phosphate synthase complex
Authors: Strohmeier, M. / Raschle, T. / Mazurkiewicz, J. / Rippe, K. / Sinning, I. / Fitzpatrick, T.B. / Tews, I.
History
DepositionNov 10, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamine amidotransferase subunit pdxT
B: Glutamine amidotransferase subunit pdxT


Theoretical massNumber of molelcules
Total (without water)42,9412
Polymers42,9412
Non-polymers00
Water7,296405
1
A: Glutamine amidotransferase subunit pdxT


Theoretical massNumber of molelcules
Total (without water)21,4711
Polymers21,4711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glutamine amidotransferase subunit pdxT


Theoretical massNumber of molelcules
Total (without water)21,4711
Polymers21,4711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.440, 81.606, 117.285
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glutamine amidotransferase subunit pdxT / Glutamine amidotransferase glutaminase subunit pdxT


Mass: 21470.607 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: strain 168 / Gene: pdxT / Plasmid: pET-BsPdx2, pET-BsYaaE / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 [DE3] / References: UniProt: P37528, EC: 2.6.-.-
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 405 / 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: 2.53 Å3/Da / Density % sol: 51.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 12.4% PEG 8000, 6% ethylene glycol, 100mM cacodylic acid, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 25, 2005 / Details: ESRF
RadiationMonochromator: ESRF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.73→50 Å / Num. all: 46456 / Num. obs: 45697 / % possible obs: 98.4 % / Redundancy: 5.3 % / Biso Wilson estimate: 28 Å2 / Rsym value: 0.065 / Net I/σ(I): 17.3
Reflection shellResolution: 1.73→1.75 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 2 / Rsym value: 0.492 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1R9G

1r9g


Resolution: 1.73→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.686 / SU ML: 0.078 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21579 2310 5.1 %RANDOM
Rwork0.17956 ---
obs0.18147 43316 98.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.489 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å20 Å20 Å2
2--1.19 Å20 Å2
3----0.34 Å2
Refine analyzeLuzzati coordinate error obs: 0.213 Å
Refinement stepCycle: LAST / Resolution: 1.73→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2892 0 0 405 3297
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223042
X-RAY DIFFRACTIONr_bond_other_d0.0020.022083
X-RAY DIFFRACTIONr_angle_refined_deg1.7061.9694111
X-RAY DIFFRACTIONr_angle_other_deg2.00735094
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7615373
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.86724.267150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.57815543
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3381524
X-RAY DIFFRACTIONr_chiral_restr0.1080.2478
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023354
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02598
X-RAY DIFFRACTIONr_nbd_refined0.2490.2642
X-RAY DIFFRACTIONr_nbd_other0.2390.22224
X-RAY DIFFRACTIONr_nbtor_refined0.1810.21482
X-RAY DIFFRACTIONr_nbtor_other0.0850.21670
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2960.2294
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.360.226
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3630.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1830.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7121.52054
X-RAY DIFFRACTIONr_mcbond_other0.1881.5775
X-RAY DIFFRACTIONr_mcangle_it2.09323042
X-RAY DIFFRACTIONr_scbond_it3.01731210
X-RAY DIFFRACTIONr_scangle_it4.5564.51069
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.73→1.775 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 177 -
Rwork0.228 3171 -
obs--99.47 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6526-0.19290.1791.0797-0.23871.1104-0.004-0.0011-0.010.05160.01590.0547-0.0529-0.1104-0.0119-0.05220.0011-0.0025-0.00940.0217-0.03231.957412.5209-23.8593
20.6582-0.0013-0.0611.03450.15610.8695-0.01970.0145-0.00140.12420.0057-0.0348-0.02680.00740.014-0.00510.0130.0005-0.05490.0146-0.0331-16.2143-9.0814-5.0789
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1951 - 195
2X-RAY DIFFRACTION2BB1 - 1941 - 194

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