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- PDB-4ads: Crystal structure of plasmodial PLP synthase complex -

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Basic information

Entry
Database: PDB / ID: 4ads
TitleCrystal structure of plasmodial PLP synthase complex
Components
  • PDX2 PROTEIN
  • PYRIDOXINE BIOSYNTHETIC ENZYME PDX1 HOMOLOGUE, PUTATIVE
KeywordsTRANSFERASE/TRANSFERASE / TRANSFERASE-TRANSFERASE COMPLEX / PYRIDOXAL 5-PHOSPHATE BIOSYNTHESIS
Function / homology
Function and homology information


vitamin B6 biosynthetic process / pyridoxine metabolic process / glutaminase complex / pyridoxal 5'-phosphate synthase (glutamine hydrolysing) / pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity / response to singlet oxygen / pyridoxal phosphate biosynthetic process / glutaminase / glutaminase activity / 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 / Aldolase class I / TIM Barrel / Alpha-Beta Barrel ...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 / Aldolase class I / TIM Barrel / Alpha-Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / : / Pyridoxal 5'-phosphate synthase subunit PDX2 / Pyridoxal 5'-phosphate synthase subunit PDX2
Similarity search - Component
Biological speciesPLASMODIUM BERGHEI (eukaryote)
PLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.61 Å
AuthorsGuedez, G. / Sinning, I. / Tews, I.
CitationJournal: Structure / Year: 2012
Title: Assembly of the Eukaryotic Plp-Synthase Complex from Plasmodium and Activation of the Pdx1 Enzyme.
Authors: Guedez, G. / Hipp, K. / Windeisen, V. / Derrer, B. / Gengenbacher, M. / Boettcher, B. / Sinning, I. / Kappes, B. / Tews, I.
History
DepositionJan 3, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "EA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "FA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PYRIDOXINE BIOSYNTHETIC ENZYME PDX1 HOMOLOGUE, PUTATIVE
B: PYRIDOXINE BIOSYNTHETIC ENZYME PDX1 HOMOLOGUE, PUTATIVE
C: PYRIDOXINE BIOSYNTHETIC ENZYME PDX1 HOMOLOGUE, PUTATIVE
D: PYRIDOXINE BIOSYNTHETIC ENZYME PDX1 HOMOLOGUE, PUTATIVE
E: PYRIDOXINE BIOSYNTHETIC ENZYME PDX1 HOMOLOGUE, PUTATIVE
F: PYRIDOXINE BIOSYNTHETIC ENZYME PDX1 HOMOLOGUE, PUTATIVE
G: PDX2 PROTEIN
H: PDX2 PROTEIN
I: PDX2 PROTEIN
J: PDX2 PROTEIN
K: PDX2 PROTEIN
L: PDX2 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)332,06824
Polymers330,92812
Non-polymers1,14012
Water724
1
A: PYRIDOXINE BIOSYNTHETIC ENZYME PDX1 HOMOLOGUE, PUTATIVE
B: PYRIDOXINE BIOSYNTHETIC ENZYME PDX1 HOMOLOGUE, PUTATIVE
C: PYRIDOXINE BIOSYNTHETIC ENZYME PDX1 HOMOLOGUE, PUTATIVE
D: PYRIDOXINE BIOSYNTHETIC ENZYME PDX1 HOMOLOGUE, PUTATIVE
E: PYRIDOXINE BIOSYNTHETIC ENZYME PDX1 HOMOLOGUE, PUTATIVE
F: PYRIDOXINE BIOSYNTHETIC ENZYME PDX1 HOMOLOGUE, PUTATIVE
G: PDX2 PROTEIN
H: PDX2 PROTEIN
I: PDX2 PROTEIN
J: PDX2 PROTEIN
K: PDX2 PROTEIN
L: PDX2 PROTEIN
hetero molecules

A: PYRIDOXINE BIOSYNTHETIC ENZYME PDX1 HOMOLOGUE, PUTATIVE
B: PYRIDOXINE BIOSYNTHETIC ENZYME PDX1 HOMOLOGUE, PUTATIVE
C: PYRIDOXINE BIOSYNTHETIC ENZYME PDX1 HOMOLOGUE, PUTATIVE
D: PYRIDOXINE BIOSYNTHETIC ENZYME PDX1 HOMOLOGUE, PUTATIVE
E: PYRIDOXINE BIOSYNTHETIC ENZYME PDX1 HOMOLOGUE, PUTATIVE
F: PYRIDOXINE BIOSYNTHETIC ENZYME PDX1 HOMOLOGUE, PUTATIVE
G: PDX2 PROTEIN
H: PDX2 PROTEIN
I: PDX2 PROTEIN
J: PDX2 PROTEIN
K: PDX2 PROTEIN
L: PDX2 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)664,13648
Polymers661,85724
Non-polymers2,27924
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area84700 Å2
ΔGint-547.1 kcal/mol
Surface area209220 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33980 Å2
ΔGint-244.6 kcal/mol
Surface area112980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.008, 160.008, 583.243
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
12G
22I
32L
13H
23J
33K

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPPO4PO4AA - N3 - 3021
21ASPASPPO4PO4BB - P3 - 3021
31ASPASPPO4PO4CC - R3 - 3021
41ASPASPPO4PO4DD - T3 - 3021
51ASPASPPO4PO4EE - V3 - 3021
61ASPASPPO4PO4FF - X3 - 3021
12GLUGLUSERSERGG3 - 2191 - 217
22GLUGLUSERSERII3 - 2191 - 217
32GLUGLUSERSERLL3 - 2191 - 217
13GLUGLUSERSERHH3 - 2191 - 217
23GLUGLUSERSERJJ3 - 2191 - 217
33GLUGLUSERSERKK3 - 2191 - 217

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
PYRIDOXINE BIOSYNTHETIC ENZYME PDX1 HOMOLOGUE, PUTATIVE


Mass: 30807.857 Da / Num. of mol.: 6 / Fragment: RESIDUES 3-282
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PLASMODIUM BERGHEI (eukaryote) / Strain: NK65 / Plasmid: PET21-A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: Q4Z0E8
#2: Protein
PDX2 PROTEIN


Mass: 24346.857 Da / Num. of mol.: 6 / Fragment: RESIDUES 3-219 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
Strain: 3D7 / Plasmid: PET21-A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: Q5ND68, UniProt: Q8IIK4*PLUS
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN G, HIS 196 TO ASN ENGINEERED RESIDUE IN CHAIN H, HIS 196 TO ASN ...ENGINEERED RESIDUE IN CHAIN G, HIS 196 TO ASN ENGINEERED RESIDUE IN CHAIN H, HIS 196 TO ASN ENGINEERED RESIDUE IN CHAIN I, HIS 196 TO ASN ENGINEERED RESIDUE IN CHAIN J, HIS 196 TO ASN ENGINEERED RESIDUE IN CHAIN K, HIS 196 TO ASN ENGINEERED RESIDUE IN CHAIN L, HIS 196 TO ASN

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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: 2.69 Å3/Da / Density % sol: 54 % / Description: NONE
Crystal growpH: 6.2
Details: 0.1 M NA/K PHOSPHATE-PHOSPHATE PH 6.2, 0.2 M NACL, 6% PEG 8000, 0.01 M L-GLUTAMINE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.62
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 5, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.62 Å / Relative weight: 1
ReflectionResolution: 3.61→50 Å / Num. obs: 47666 / % possible obs: 96.8 % / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 6.41
Reflection shellResolution: 3.6→3.66 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 1.7 / % possible all: 64.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ABW

2abw


Resolution: 3.61→50 Å / Cor.coef. Fo:Fc: 0.816 / Cor.coef. Fo:Fc free: 0.79 / SU B: 110.297 / SU ML: 0.726 / Cross valid method: THROUGHOUT / ESU R Free: 0.812 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.31374 2560 5.1 %RANDOM
Rwork0.29338 ---
obs0.29442 47666 96.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 95.946 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å20.35 Å20 Å2
2--0.71 Å20 Å2
3----1.06 Å2
Refinement stepCycle: LAST / Resolution: 3.61→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23088 0 60 4 23152
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02223526
X-RAY DIFFRACTIONr_bond_other_d0.0020.0215774
X-RAY DIFFRACTIONr_angle_refined_deg1.2341.96631788
X-RAY DIFFRACTIONr_angle_other_deg2.02338778
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.63552982
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.52825.031002
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.507154230
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.06315102
X-RAY DIFFRACTIONr_chiral_restr0.0650.23666
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0225998
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024452
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: tight positional / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A36370.02
12B36370.02
13C36370.02
14D36370.02
15E36370.02
16F36370.02
21G28500.02
22I28500.02
23L28500.02
31H28500.03
32J28500.03
33K28500.02
LS refinement shellResolution: 3.612→3.705 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 160 -
Rwork0.369 2943 -
obs--83.01 %
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)
13.8881-0.20750.39390.2990.40333.25990.1064-0.27340.28860.26010.00510.0707-0.053-0.1111-0.11150.44730.0660.21560.21350.11970.362371.1795.2932-32.4033
21.2184-1.10630.8383.2541-0.753.08270.0359-0.21950.29730.1135-0.2269-0.1481-0.33080.03260.1910.197-0.02610.0390.45680.19760.3139100.3494-20.5177-31.1701
32.16031.9455-0.22022.577-1.02722.88240.0227-0.14690.0598-0.1048-0.1066-0.145-0.28260.0480.0840.10520.05240.09170.49470.30960.269892.8833-58.2024-25.2593
45.5208-1.029-0.93490.4315-0.07783.7027-0.0233-0.0634-0.2517-0.05880.0362-0.0312-0.07680.2816-0.01290.09070.11040.13850.41040.32080.335356.2157-70.3719-20.5934
51.3763-1.5992-0.5353.63250.2284.04260.06030.0059-0.2090.0417-0.03360.06330.02910.1304-0.02670.03280.09730.05860.40480.3290.331327.0309-44.8161-21.665
61.30561.3498-0.05154.57211.38842.3527-0.1634-0.1668-0.02480.01420.23510.2381-0.0997-0.0276-0.07170.35280.13470.21810.32830.22910.227334.7315-7.0233-27.7519
76.0875-1.4686-1.4165.5858-0.09714.4108-0.3357-0.0735-1.0337-0.21810.0527-0.02310.89390.12660.2830.8916-0.090.15780.90140.43831.108245.6529-94.5541-10.7745
83.4125-1.3431-0.246512.7011-3.21348.73620.32350.094-0.2044-0.3052-0.31590.49460.7992-0.2231-0.00760.29690.03530.06770.93190.48860.5160.2029-45.9216-12.9654
94.9658-0.80961.339311.43930.76513.5629-0.0284-0.14650.6685-0.312-0.4087-0.3711-1.15590.4280.43710.66920.0108-0.04171.24370.39761.0447128.2498-17.7574-28.725
106.6992-1.1361-0.7046.875-0.47464.18180.16830.3495-0.2795-0.52180.0038-0.8772-0.28130.5092-0.1720.41490.0778-0.02310.72130.31290.564109.372-79.7469-17.9457
114.57922.9933-0.95898.5893-2.31356.086-0.028-0.32990.3567-0.1698-0.03660.84320.0352-0.82630.06460.93620.20010.16810.7460.14820.79418.796415.8101-24.8432
121.723-2.03210.45324.818-0.2450.2265-0.36470.47870.8331-0.11340.0877-0.2552-0.42070.10840.2771.2295-0.23440.06730.84340.16680.939482.854931.0008-30.9346
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 302
2X-RAY DIFFRACTION2B3 - 302
3X-RAY DIFFRACTION3C3 - 302
4X-RAY DIFFRACTION4D3 - 302
5X-RAY DIFFRACTION5E3 - 302
6X-RAY DIFFRACTION6F3 - 302
7X-RAY DIFFRACTION7G3 - 219
8X-RAY DIFFRACTION8H3 - 219
9X-RAY DIFFRACTION9I3 - 219
10X-RAY DIFFRACTION10J3 - 219
11X-RAY DIFFRACTION11K3 - 219
12X-RAY DIFFRACTION12L3 - 219

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