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- PDB-4c5m: Structure of the pyridoxal kinase from Staphylococcus aureus in c... -

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Basic information

Entry
Database: PDB / ID: 4c5m
TitleStructure of the pyridoxal kinase from Staphylococcus aureus in complex with AMP-PCP
ComponentsPHOSPHOMETHYLPYRIMIDINE KINASE
KeywordsTRANSFERASE / RIBOKINASE
Function / homology
Function and homology information


phosphomethylpyrimidine kinase activity / pyridoxal kinase / thiamine biosynthetic process / phosphorylation / 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
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / 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)122,90125
Polymers119,2474
Non-polymers3,65421
Water17,619978
1
B: PHOSPHOMETHYLPYRIMIDINE KINASE
D: PHOSPHOMETHYLPYRIMIDINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,49913
Polymers59,6242
Non-polymers1,87511
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6960 Å2
ΔGint-133.5 kcal/mol
Surface area19700 Å2
MethodPISA
2
A: PHOSPHOMETHYLPYRIMIDINE KINASE
C: PHOSPHOMETHYLPYRIMIDINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,40312
Polymers59,6242
Non-polymers1,77910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6740 Å2
ΔGint-126.1 kcal/mol
Surface area19790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.210, 100.510, 167.060
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(0.9995, 0.0026, 0.031), (-0.0041, 0.9988, 0.0484), (-0.0309, -0.0485, 0.9983)-1.1496, 1.2062, 42.8317
2given(-0.9843, 0.004, 0.1762), (-0.0039, -1, 0.001), (0.1762, 0.0003, 0.9844)37.7097, -5.6668, -3.4098
3given(-0.9895, -0.0332, 0.1408), (0.0226, -0.9968, -0.0764), (0.1429, -0.0725, 0.9871)45.7925, -9.629, 38.6991

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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-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 978 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFIRST AMINOACID 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: 2.19 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growDetails: 50MM HEPES, 2M NH4SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / 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: 1.45→48.76 Å / Num. obs: 185724 / % possible obs: 99.5 % / Observed criterion σ(I): 1.5 / Redundancy: 8.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 20.38
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 8.5 % / Rmerge(I) obs: 1.17 / Mean I/σ(I) obs: 1.79 / % possible all: 96.3

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4C5J

4c5j


Resolution: 1.45→48.76 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.972 / SU B: 2.323 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.17056 9325 5 %RANDOM
Rwork0.12197 ---
obs0.12442 175767 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.882 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å20 Å2
2---0.34 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.45→48.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8263 0 209 978 9450
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.028931
X-RAY DIFFRACTIONr_bond_other_d0.0010.028386
X-RAY DIFFRACTIONr_angle_refined_deg1.7232.00112226
X-RAY DIFFRACTIONr_angle_other_deg0.831319421
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.17151161
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.83926.138347
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.732151513
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.2821511
X-RAY DIFFRACTIONr_chiral_restr0.0940.21396
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029941
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021834
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_it2.8611.9054450
X-RAY DIFFRACTIONr_mcbond_other2.8621.9054449
X-RAY DIFFRACTIONr_mcangle_it3.2712.8695570
X-RAY DIFFRACTIONr_mcangle_other3.272.875571
X-RAY DIFFRACTIONr_scbond_it4.1052.2744481
X-RAY DIFFRACTIONr_scbond_other3.8792.2324414
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5873.2276519
X-RAY DIFFRACTIONr_long_range_B_refined4.76417.26510867
X-RAY DIFFRACTIONr_long_range_B_other4.41716.44110344
X-RAY DIFFRACTIONr_rigid_bond_restr3.458317317
X-RAY DIFFRACTIONr_sphericity_free28.5355222
X-RAY DIFFRACTIONr_sphericity_bonded13.583517897
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 706 -
Rwork0.202 12677 -
obs--98.62 %

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