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- PDB-2abw: Glutaminase subunit of the plasmodial PLP synthase (Vitamin B6 bi... -

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Basic information

Entry
Database: PDB / ID: 2abw
TitleGlutaminase subunit of the plasmodial PLP synthase (Vitamin B6 biosynthesis)
ComponentsPdx2 protein
KeywordsTRANSFERASE / Glutaminase / PLP-synthase / Vitamin B6 / malaria
Function / homology
Function and homology information


vitamin B6 biosynthetic process / pyridoxal 5'-phosphate synthase (glutamine hydrolysing) / pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity / response to singlet oxygen / pyridoxal phosphate biosynthetic process / glutaminase / glutaminase activity / glutamine metabolic process / 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 PDX2
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsGengenbacher, M. / Fitzpatrick, T.B. / Raschle, T. / Flicker, K. / Sinning, I. / Mueller, S. / Macheroux, P. / Tews, I. / Kappes, B.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Vitamin B6 Biosynthesis by the Malaria Parasite Plasmodium falciparum: Biochemical and structural insights
Authors: Gengenbacher, M. / Fitzpatrick, T.B. / Raschle, T. / Flicker, K. / Sinning, I. / Mueller, S. / Macheroux, P. / Tews, I. / Kappes, B.
History
DepositionJul 17, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 10, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 25, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Pdx2 protein
B: Pdx2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5153
Polymers51,3212
Non-polymers1941
Water8,449469
1
A: Pdx2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8552
Polymers25,6601
Non-polymers1941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pdx2 protein


Theoretical massNumber of molelcules
Total (without water)25,6601
Polymers25,6601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.042, 67.917, 70.327
Angle α, β, γ (deg.)90.00, 92.31, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1137-

HOH

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Components

#1: Protein Pdx2 protein / Glutaminase


Mass: 25660.330 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: Pdx2 / Plasmid: pET21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3)-RIL
References: GenBank: 56797978, UniProt: Q8IIK4*PLUS, EC: 2.6.-.-
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 469 / 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 Å3/Da / Density % sol: 39.5 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 30% PEG200, 5% PEG8000 buffered with 2-(N-morpholino)ethanesulfonic acid (MES), pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 28, 2004
RadiationMonochromator: ESRF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.62→25 Å / Num. all: 52687 / Num. obs: 52658 / % possible obs: 99.9 % / Observed criterion σ(F): 20 / Observed criterion σ(I): -4 / Redundancy: 5.2 % / Rmerge(I) obs: 0.064 / Χ2: 1 / Net I/σ(I): 19.25
Reflection shellResolution: 1.62→1.63 Å / % possible obs: 100 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.466 / Mean I/σ(I) obs: 2.25 / Num. measured obs: 1362 / Χ2: 1 / % possible all: 100

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Phasing

Phasing MRRfactor: 0.556 / Cor.coef. Fo:Fc: 0.236
Highest resolutionLowest resolution
Rotation3 Å24.9 Å
Translation3 Å24.9 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT1.7data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R9G CHAIN A

1r9g


Resolution: 1.62→25 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.222 / WRfactor Rwork: 0.179 / SU B: 3.337 / SU ML: 0.058 / TLS residual ADP flag: LIKELY RESIDUAL / ESU R: 0.088 / ESU R Free: 0.09 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.1892 2676 5.082 %
Rwork0.1515 --
all0.153 --
obs0.153 52656 99.941 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 19.129 Å2
Baniso -1Baniso -2Baniso -3
1-0.214 Å20 Å2-0.161 Å2
2--0.309 Å20 Å2
3----0.536 Å2
Refinement stepCycle: LAST / Resolution: 1.62→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3483 0 13 469 3965
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0223760
X-RAY DIFFRACTIONr_bond_other_d0.0020.022511
X-RAY DIFFRACTIONr_angle_refined_deg1.9621.9475122
X-RAY DIFFRACTIONr_angle_other_deg1.05636188
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9435466
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.32524.483174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.70515647
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.781514
X-RAY DIFFRACTIONr_chiral_restr0.1270.2587
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024168
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02753
X-RAY DIFFRACTIONr_nbd_refined0.2790.2854
X-RAY DIFFRACTIONr_nbd_other0.2260.22786
X-RAY DIFFRACTIONr_nbtor_refined0.1880.21937
X-RAY DIFFRACTIONr_nbtor_other0.0890.21982
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2280.2373
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.242
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2340.295
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2620.257
X-RAY DIFFRACTIONr_mcbond_it2.0291.53037
X-RAY DIFFRACTIONr_mcbond_other0.3851.5927
X-RAY DIFFRACTIONr_mcangle_it2.17923765
X-RAY DIFFRACTIONr_mcangle_other1.02423101
X-RAY DIFFRACTIONr_scbond_it3.58431814
X-RAY DIFFRACTIONr_scbond_other1.33332309
X-RAY DIFFRACTIONr_scangle_it4.4214.51349
X-RAY DIFFRACTIONr_scangle_other2.2584.53087
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.62-1.6620.2281680.1913715388599.949
1.662-1.7070.2371900.1763544373599.973
1.707-1.7560.2192000.1653493369499.973
1.756-1.810.2011830.15433793562100
1.81-1.8690.1932040.15432313435100
1.869-1.9350.1821490.14731933342100
1.935-2.0070.1911620.14730693231100
2.007-2.0880.1851570.14429483105100
2.088-2.1810.1891520.1382806295999.966
2.181-2.2860.1841440.142729287499.965
2.286-2.4090.2011380.14725852723100
2.409-2.5530.1791130.15224402553100
2.553-2.7280.1921180.14923122430100
2.728-2.9430.1721310.162151228399.956
2.943-3.220.2211010.15719482049100
3.22-3.5920.167830.14318201903100
3.592-4.1340.1961020.1415811683100
4.134-5.0290.144690.13213721441100
5.029-6.9720.246660.18810581124100
6.972-250.152460.18860667696.45
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)
10.7169-0.1510.04220.66210.19320.6584-0.0130.02990.0222-0.08720.0218-0.0122-0.05430.062-0.0088-0.027-0.00850.0142-0.02080.0081-0.02769.984667.661320.1696
20.4088-0.08830.04541.384-0.26660.43360.00520.0236-0.0431-0.04370.0170.10290.08770.0347-0.0222-0.02170.0221-0.0093-0.0373-0.0017-0.030311.182236.188115.2946
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA2 - 2212 - 221
22BB2 - 2272 - 227

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