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- PDB-6su9: Crystal structure of Plasmodium falciparum PdxK with ligands AMP-... -

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Basic information

Entry
Database: PDB / ID: 6su9
TitleCrystal structure of Plasmodium falciparum PdxK with ligands AMP-PNP and PL
ComponentsPyridoxal kinase
KeywordsTRANSFERASE / Crystal structure of Plasmodium falciparum PdxK with ligands AMP-PNP and PL.
Function / homology
Function and homology information


pyridoxamine binding / pyridoxine binding / Vitamin B6 activation to pyridoxal phosphate / vitamin B6 biosynthetic process / pyridoxal binding / pyridoxine metabolic process / pyridoxal kinase activity / pyridoxal 5'-phosphate salvage / pyridoxal kinase / response to singlet oxygen ...pyridoxamine binding / pyridoxine binding / Vitamin B6 activation to pyridoxal phosphate / vitamin B6 biosynthetic process / pyridoxal binding / pyridoxine metabolic process / pyridoxal kinase activity / pyridoxal 5'-phosphate salvage / pyridoxal kinase / response to singlet oxygen / Neutrophil degranulation / phosphorylation / ATP binding / metal ion binding / cytosol
Similarity search - Function
Pyridoxine kinase / Pyridoxamine kinase/Phosphomethylpyrimidine kinase / Phosphomethylpyrimidine kinase / Ribokinase-like
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Chem-PXL / pyridoxal kinase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsGroves, M.R. / Gao, K. / Wang, W.
CitationJournal: Crystals / Year: 2019
Title: Crystal structure of Plasmodium falciparum PdxK with ligands AMP-PNP and PL.
Authors: Gao, K. / Wang, W. / Groves, M.R.
History
DepositionSep 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pyridoxal kinase
B: Pyridoxal kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,9759
Polymers114,5552
Non-polymers1,4207
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6250 Å2
ΔGint-42 kcal/mol
Surface area22990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.703, 62.004, 93.712
Angle α, β, γ (deg.)90.000, 94.990, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Pyridoxal kinase


Mass: 57277.742 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / Gene: PF3D7_0616000 / Production host: Escherichia coli (E. coli) / References: UniProt: C6KT01, pyridoxal kinase
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-PXL / 3-HYDROXY-5-(HYDROXYMETHYL)-2-METHYLISONICOTINALDEHYDE / PYRIDOXAL


Mass: 167.162 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H9NO3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.25 Å3/Da / Density % sol: 56.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 0.1 M HEPES pH 7.75, 0.2 M CaCl2, 31%(v/v) PEG400, 5%(v/v) glycerol
PH range: 7.0-8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.15→19.33 Å / Num. obs: 32284 / % possible obs: 97.87 % / Redundancy: 2.55 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 2
Reflection shellResolution: 2.15→2.227 Å / Rmerge(I) obs: 0.042 / Num. unique obs: 3159 / % possible all: 97.17

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RFU

1rfu


Resolution: 2.15→19.327 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.93
RfactorNum. reflection% reflection
Rfree0.2719 1627 5.04 %
Rwork0.2094 --
obs0.2126 32276 98.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 131.43 Å2 / Biso mean: 59.7016 Å2 / Biso min: 20.85 Å2
Refinement stepCycle: final / Resolution: 2.15→19.327 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4727 0 89 69 4885
Biso mean--73.01 54.41 -
Num. residues----587
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084896
X-RAY DIFFRACTIONf_angle_d0.9526619
X-RAY DIFFRACTIONf_chiral_restr0.058763
X-RAY DIFFRACTIONf_plane_restr0.005819
X-RAY DIFFRACTIONf_dihedral_angle_d6.822906
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.15-2.21320.38581420.3053250797
2.2132-2.28450.37421320.2904252897
2.2845-2.3660.31951470.2671249498
2.366-2.46060.31071210.2521255798
2.4606-2.57230.29471280.2332251998
2.5723-2.70760.30661490.2371254398
2.7076-2.87670.34961290.2507255798
2.8767-3.0980.33551300.2541258498
3.098-3.40820.29911300.2331255099
3.4082-3.89790.25621390.2024257798
3.8979-4.89770.23281400.1581258298
4.8977-19.3270.2131400.1762265199
Refinement TLS params.Method: refined / Origin x: 57.9389 Å / Origin y: -0.6275 Å / Origin z: 23.2296 Å
111213212223313233
T0.2855 Å2-0.0415 Å2-0.1198 Å2-0.4328 Å20.0054 Å2--0.2375 Å2
L4.1865 °2-1.8734 °2-2.592 °2-2.3067 °21.6897 °2--3.1963 °2
S0.1385 Å °0.7643 Å °-0.0547 Å °-0.289 Å °-0.1767 Å °0.0436 Å °-0.1442 Å °-0.2194 Å °0.0354 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 1001
2X-RAY DIFFRACTION1allB1 - 601
3X-RAY DIFFRACTION1allS1 - 126
4X-RAY DIFFRACTION1allC1 - 3

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