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- PDB-4c5k: Structure of the pyridoxal kinase from Staphylococcus aureus in c... -

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Basic information

Entry
Database: PDB / ID: 4c5k
TitleStructure of the pyridoxal kinase from Staphylococcus aureus in complex with ADP
ComponentsPHOSPHOMETHYLPYRIMIDINE KINASE
KeywordsTRANSFERASE / RIBOKINASE
Function / homology
Function and homology information


phosphomethylpyrimidine kinase activity / pyridoxal kinase / thiamine biosynthetic process / nucleotide binding
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
ADENOSINE-5'-DIPHOSPHATE / pyridoxal kinase / Phosphomethylpyrimidine kinase
Similarity search - Component
Biological speciesSTAPHYLOCOCCUS AUREUS SUBSP. AUREUS MU50 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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)122,20521
Polymers119,2474
Non-polymers2,95817
Water16,646924
1
B: PHOSPHOMETHYLPYRIMIDINE KINASE
D: PHOSPHOMETHYLPYRIMIDINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,15011
Polymers59,6242
Non-polymers1,5279
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6470 Å2
ΔGint-121.8 kcal/mol
Surface area19820 Å2
MethodPISA
2
A: PHOSPHOMETHYLPYRIMIDINE KINASE
C: PHOSPHOMETHYLPYRIMIDINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,05410
Polymers59,6242
Non-polymers1,4318
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6320 Å2
ΔGint-113.3 kcal/mol
Surface area19540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.460, 100.360, 167.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.9991, -0.0069, 0.0417), (0.0053, 0.9993, 0.0376), (-0.0419, -0.0373, 0.9984)-0.3017, 0.2231, 43.1731
2given(-0.9845, 0.0097, 0.1754), (-0.0113, -0.9999, -0.008), (0.1753, -0.0099, 0.9845)37.6815, -5.8369, -3.4252
3given(-0.9916, -0.0162, 0.1285), (0.0051, -0.9963, -0.0863), (0.1294, -0.0849, 0.9879)44.9982, -9.9277, 39.1265

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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-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 924 / 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: 2.2 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growDetails: 50MM HEPES, 2M NAH4SO4

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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: Jul 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→48.78 Å / Num. obs: 200707 / % possible obs: 97.1 % / Observed criterion σ(I): 1 / Redundancy: 8.9 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 23.35
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.98 / Mean I/σ(I) obs: 2 / % possible all: 93.1

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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 4C5J

4c5j


Resolution: 1.4→48.78 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.884 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16519 10053 5 %RANDOM
Rwork0.12794 ---
obs0.12983 190654 97.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.569 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2---0 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.4→48.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8259 0 173 924 9356
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.028749
X-RAY DIFFRACTIONr_bond_other_d0.0010.028269
X-RAY DIFFRACTIONr_angle_refined_deg1.7181.98611934
X-RAY DIFFRACTIONr_angle_other_deg0.901319123
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.38751138
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.72826.14342
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.984151477
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.5971510
X-RAY DIFFRACTIONr_chiral_restr0.1050.21385
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029841
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021817
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_it2.991.8824427
X-RAY DIFFRACTIONr_mcbond_other2.991.8824426
X-RAY DIFFRACTIONr_mcangle_it3.3592.8355537
X-RAY DIFFRACTIONr_mcangle_other3.3592.8355538
X-RAY DIFFRACTIONr_scbond_it4.0142.2434322
X-RAY DIFFRACTIONr_scbond_other3.8842.2164267
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5243.1996290
X-RAY DIFFRACTIONr_long_range_B_refined4.72416.83410618
X-RAY DIFFRACTIONr_long_range_B_other4.37816.14810156
X-RAY DIFFRACTIONr_rigid_bond_restr4.251317018
X-RAY DIFFRACTIONr_sphericity_free31.2085233
X-RAY DIFFRACTIONr_sphericity_bonded13.802517540
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 719 -
Rwork0.249 13343 -
obs--92.9 %

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