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- PDB-4c5j: Structure of the pyridoxal kinase from Staphylococcus aureus -

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Basic information

Entry
Database: PDB / ID: 4c5j
TitleStructure of the pyridoxal kinase from Staphylococcus aureus
ComponentsPHOSPHOMETHYLPYRIMIDINE KINASE
KeywordsTRANSFERASE / RIBOKINASE
Function / homology
Function and homology information


phosphomethylpyrimidine kinase activity / hydroxymethylpyrimidine kinase activity / pyridoxal kinase / thiamine biosynthetic process / nucleotide binding / cytosol
Similarity search - Function
Hydroxymethylpyrimidine kinase/phosphomethylpyrimidine kinase / Hydroxymethylpyrimidine kinase/phosphomethylpyrimidine kinase domain / Pyridoxamine kinase/Phosphomethylpyrimidine kinase / Phosphomethylpyrimidine kinase / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
pyridoxal kinase / Phosphomethylpyrimidine kinase
Similarity search - Component
Biological speciesSTAPHYLOCOCCUS AUREUS SUBSP. AUREUS MU50 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsNodwell, M. / Alte, F. / Sieber, S.A. / Schneider, S.
CitationJournal: J.Am.Chem.Soc. / Year: 2014
Title: A Subfamily of Bacterial Ribokinases Utilizes a Hemithioacetal for Pyridoxal Phosphate Salvage.
Authors: Nodwell, M.B. / Koch, M.F. / Alte, F. / Schneider, S. / Sieber, S.A.
History
DepositionSep 12, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2014Group: Database references
Revision 1.2Dec 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_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_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: PHOSPHOMETHYLPYRIMIDINE KINASE
B: PHOSPHOMETHYLPYRIMIDINE KINASE
C: PHOSPHOMETHYLPYRIMIDINE KINASE
D: PHOSPHOMETHYLPYRIMIDINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,59218
Polymers119,2474
Non-polymers1,34514
Water17,871992
1
A: PHOSPHOMETHYLPYRIMIDINE KINASE
D: PHOSPHOMETHYLPYRIMIDINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2969
Polymers59,6242
Non-polymers6727
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-114.1 kcal/mol
Surface area20220 Å2
MethodPISA
2
B: PHOSPHOMETHYLPYRIMIDINE KINASE
C: PHOSPHOMETHYLPYRIMIDINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2969
Polymers59,6242
Non-polymers6727
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint-115.5 kcal/mol
Surface area20380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.580, 102.340, 83.540
Angle α, β, γ (deg.)90.00, 90.98, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.9982, -0.0027, 0.0592), (-0.0039, -0.9938, -0.1114), (0.0592, -0.1115, 0.992)-26.2936, 6.8658, 42.2048
2given(0.9995, 0.005, -0.0299), (-0.0058, 0.9997, -0.0244), (0.0297, 0.0246, 0.9993)-21.4235, -8.3816, -67.0049
3given(-0.9998, -0.0089, 0.0196), (0.0062, -0.991, -0.1339), (0.0206, -0.1338, 0.9908)-24.1628, 11.0365, 0.9919

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Components

#1: Protein
PHOSPHOMETHYLPYRIMIDINE KINASE / PYRIDOXAL KINASE


Mass: 29811.793 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STAPHYLOCOCCUS AUREUS SUBSP. AUREUS MU50 (bacteria)
Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q99W31, UniProt: A0A0H3JTP0*PLUS, pyridoxal kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 992 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFIRST AMINO ACID IS A GLY INSTEAD OF MET DUE TO REMOVAL OF THE AFFINITY TAG

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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: 2.28 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growDetails: 50 MM HEPES, PH 7.6, 2M AMMONIUM SULPHATE 10MG/ML PROTEIN

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: May 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→45.69 Å / Num. obs: 183201 / % possible obs: 97.1 % / Observed criterion σ(I): 1.5 / Redundancy: 4.5 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.93
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 1.87 / % possible all: 93

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2I5B

2i5b


Resolution: 1.45→45.69 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.972 / SU B: 2.477 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17811 9265 5.1 %RANDOM
Rwork0.13004 ---
obs0.1325 173936 97.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.437 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20 Å2-0.46 Å2
2---1.06 Å20 Å2
3---0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.45→45.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8290 0 70 992 9352
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0198606
X-RAY DIFFRACTIONr_bond_other_d0.0010.028185
X-RAY DIFFRACTIONr_angle_refined_deg1.8021.96911706
X-RAY DIFFRACTIONr_angle_other_deg0.905318928
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.11951132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.43326.257342
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.995151466
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.757158
X-RAY DIFFRACTIONr_chiral_restr0.1240.21361
X-RAY DIFFRACTIONr_gen_planes_refined0.010.029771
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021781
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_it3.5351.8244429
X-RAY DIFFRACTIONr_mcbond_other3.5331.8244428
X-RAY DIFFRACTIONr_mcangle_it4.3162.7455537
X-RAY DIFFRACTIONr_mcangle_other4.3172.7465538
X-RAY DIFFRACTIONr_scbond_it5.2832.2744177
X-RAY DIFFRACTIONr_scbond_other4.9832.2274121
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7033.1796066
X-RAY DIFFRACTIONr_long_range_B_refined5.58316.60410538
X-RAY DIFFRACTIONr_long_range_B_other5.2815.7879982
X-RAY DIFFRACTIONr_rigid_bond_restr5.817316791
X-RAY DIFFRACTIONr_sphericity_free26.4635236
X-RAY DIFFRACTIONr_sphericity_bonded13.697517391
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 628 -
Rwork0.277 12325 -
obs--92.89 %

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