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- PDB-1vi9: Crystal structure of pyridoxamine kinase -

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Basic information

Entry
Database: PDB / ID: 1vi9
TitleCrystal structure of pyridoxamine kinase
ComponentsPyridoxamine kinase
KeywordsTRANSFERASE / structural genomics
Function / homology
Function and homology information


vitamin B6 biosynthetic process / pyridoxal metabolic process / pyridoxal kinase activity / pyridoxal 5'-phosphate salvage / pyridoxal kinase / magnesium ion binding / protein homodimerization activity / ATP binding / cytosol
Similarity search - Function
Pyridoxal kinase PdxY / Pyridoxine kinase / 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
BETA-MERCAPTOETHANOL / Pyridoxal kinase PdxY
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Se-Met MAD phasing / Resolution: 1.96 Å
AuthorsStructural GenomiX
CitationJournal: Proteins / Year: 2005
Title: Structural analysis of a set of proteins resulting from a bacterial genomics project
Authors: Badger, J. / Sauder, J.M. / Adams, J.M. / Antonysamy, S. / Bain, K. / Bergseid, M.G. / Buchanan, S.G. / Buchanan, M.D. / Batiyenko, Y. / Christopher, J.A. / Emtage, S. / Eroshkina, A. / ...Authors: Badger, J. / Sauder, J.M. / Adams, J.M. / Antonysamy, S. / Bain, K. / Bergseid, M.G. / Buchanan, S.G. / Buchanan, M.D. / Batiyenko, Y. / Christopher, J.A. / Emtage, S. / Eroshkina, A. / Feil, I. / Furlong, E.B. / Gajiwala, K.S. / Gao, X. / He, D. / Hendle, J. / Huber, A. / Hoda, K. / Kearins, P. / Kissinger, C. / Laubert, B. / Lewis, H.A. / Lin, J. / Loomis, K. / Lorimer, D. / Louie, G. / Maletic, M. / Marsh, C.D. / Miller, I. / Molinari, J. / Muller-Dieckmann, H.J. / Newman, J.M. / Noland, B.W. / Pagarigan, B. / Park, F. / Peat, T.S. / Post, K.W. / Radojicic, S. / Ramos, A. / Romero, R. / Rutter, M.E. / Sanderson, W.E. / Schwinn, K.D. / Tresser, J. / Winhoven, J. / Wright, T.A. / Wu, L. / Xu, J. / Harris, T.J.
History
DepositionDec 1, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn.ptnr2_label_seq_id / _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: Pyridoxamine kinase
B: Pyridoxamine kinase
C: Pyridoxamine kinase
D: Pyridoxamine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,22710
Polymers132,6864
Non-polymers5416
Water16,628923
1
A: Pyridoxamine kinase
B: Pyridoxamine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,6135
Polymers66,3432
Non-polymers2703
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-58 kcal/mol
Surface area20930 Å2
MethodPISA, PQS
2
C: Pyridoxamine kinase
D: Pyridoxamine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,6135
Polymers66,3432
Non-polymers2703
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-55 kcal/mol
Surface area20600 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)53.383, 92.592, 122.237
Angle α, β, γ (deg.)90.00, 99.42, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Pyridoxamine kinase / PM kinase


Mass: 33171.613 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PDXY, B1636 / Production host: Escherichia coli (E. coli) / References: UniProt: P77150, pyridoxal kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 923 / Source method: isolated from a natural source / Formula: H2O

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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: 45.24 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mMHEPES1droppH7.5
2150 mM1dropNaCl
310 mMmethionine1drop
410 %glycerol1drop
55 mMdithiothreitol1drop
610 mg/mlprotein1drop

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 0.9795, 0.9641
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: MAD / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.96411
ReflectionResolution: 1.96→43.03 Å / Num. all: 83507 / Num. obs: 83507 / % possible obs: 98.9 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.182 / Net I/σ(I): 7.4
Reflection shellResolution: 1.96→2.06 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.01224 / Mean I/σ(I) obs: 1.3 / % possible all: 92.8
Reflection shell
*PLUS
% possible obs: 92.8 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
TRUNCATEdata reduction
REFMAC4refinement
CCP4(SCALAdata scaling
TRUNCATEdata scaling
RefinementMethod to determine structure: Se-Met MAD phasing / Resolution: 1.96→43.03 Å / σ(F): 0
RfactorNum. reflection
Rfree0.256 4167
Rwork0.198 -
obs-83506
Solvent computationSolvent model: Babinet bulk solvent correction / Bsol: 389.512 Å2 / ksol: 0.996 e/Å3
Displacement parametersBiso mean: 26.787 Å2
Baniso -1Baniso -2Baniso -3
1--0.776 Å20 Å2-0.168 Å2
2--0.41 Å20 Å2
3---0.311 Å2
Refine Biso Class: all / Treatment: isotropic
Refinement stepCycle: LAST / Resolution: 1.96→43.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8794 0 28 923 9745
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.012
X-RAY DIFFRACTIONp_angle_d2.195
X-RAY DIFFRACTIONp_planar_tor2.565
X-RAY DIFFRACTIONp_chiral_restr0.136
X-RAY DIFFRACTIONp_plane_restr0.012
X-RAY DIFFRACTIONp_mcbond_it1.535
X-RAY DIFFRACTIONp_mcangle_it2.515
X-RAY DIFFRACTIONp_scbond_it2.89
X-RAY DIFFRACTIONp_scangle_it3.951
Software
*PLUS
Version: 4 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.2

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