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- PDB-2i5b: The crystal structure of an ADP complex of Bacillus subtilis pyri... -

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Basic information

Entry
Database: PDB / ID: 2i5b
TitleThe crystal structure of an ADP complex of Bacillus subtilis pyridoxal kinase provides evidence for the parralel emergence of enzyme activity during evolution
ComponentsPhosphomethylpyrimidine kinase
KeywordsTRANSFERASE / ADP complex / PdxK / thiD / ribokinase superfamily
Function / homology
Function and homology information


phosphomethylpyrimidine kinase activity / hydroxymethylpyrimidine kinase activity / pyridoxal kinase activity / pyridoxal kinase / thiamine biosynthetic process / ATP binding / metal ion binding / cytosol
Similarity search - Function
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 / Pyridoxine kinase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsNewman, J.A. / Das, S.K. / Sedelnikova, S.E. / Rice, D.W.
Citation
Journal: J.Mol.Biol. / Year: 2006
Title: The Crystal Structure of an ADP Complex of Bacillus subtilis Pyridoxal Kinase Provides Evidence for the Parallel Emergence of Enzyme Activity During Evolution.
Authors: Newman, J.A. / Das, S.K. / Sedelnikova, S.E. / Rice, D.W.
#1: Journal: To be published
Title: Cloning, purification and preliminary crystallographic analysis of a putative Pyridoxal Kinase from Bacillus subtilis
History
DepositionAug 24, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 30, 2023Group: 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphomethylpyrimidine kinase
C: Phosphomethylpyrimidine kinase
D: Phosphomethylpyrimidine kinase
B: Phosphomethylpyrimidine kinase
E: Phosphomethylpyrimidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,37210
Polymers145,2365
Non-polymers2,1365
Water00
1
A: Phosphomethylpyrimidine kinase
B: Phosphomethylpyrimidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9494
Polymers58,0942
Non-polymers8542
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-34 kcal/mol
Surface area19480 Å2
MethodPISA
2
C: Phosphomethylpyrimidine kinase
D: Phosphomethylpyrimidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9494
Polymers58,0942
Non-polymers8542
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-35 kcal/mol
Surface area19440 Å2
MethodPISA
3
E: Phosphomethylpyrimidine kinase
hetero molecules

E: Phosphomethylpyrimidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9494
Polymers58,0942
Non-polymers8542
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Unit cell
Length a, b, c (Å)102.499, 102.499, 251.360
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
12B
13C
14D
/ NCS ensembles :
IDDetails
1A
2B
3C
4D
DetailsThe biological assembly is a dimer formed between chanis A and B and by chains C and D

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Components

#1: Protein
Phosphomethylpyrimidine kinase / HMP-phosphate kinase / HMP-P kinase


Mass: 29047.225 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: thiD / Plasmid: pTB361 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P39610, phosphooxymethylpyrimidine kinase
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
Has protein modificationY

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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: 2.27 Å3/Da / Density % sol: 45.86 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 28% peg 4000, 0.17M sodium acetate trihydrate, 0.1M Tris HCL (pH 8.5), 10mM MgCl, 10mM ADP, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 9, 2005
RadiationMonochromator: Osmic Varimax mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.8→94.916 Å / Num. all: 33604 / Num. obs: 33604 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 50.3 Å2 / Rmerge(I) obs: 0.131 / Rsym value: 0.131 / Net I/σ(I): 5.7
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 1.7 / Num. measured all: 18268 / Num. unique all: 4844 / Rsym value: 0.475 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
MAR345345DTBdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UB0

1ub0


Resolution: 2.8→12.87 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.865 / SU B: 15.994 / SU ML: 0.317 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.441 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.274 1688 5.1 %RANDOM
Rwork0.222 ---
all0.225 33305 --
obs0.225 33305 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.436 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: LAST / Resolution: 2.8→12.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9932 0 135 0 10067
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02210231
X-RAY DIFFRACTIONr_angle_refined_deg1.4551.98613911
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.29551320
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.8526.492382
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.133151773
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.0381515
X-RAY DIFFRACTIONr_chiral_restr0.0940.21669
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027408
X-RAY DIFFRACTIONr_nbd_refined0.2190.24919
X-RAY DIFFRACTIONr_nbtor_refined0.3110.26999
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2331
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3580.2108
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.430.28
X-RAY DIFFRACTIONr_mcbond_it0.5761.56721
X-RAY DIFFRACTIONr_mcangle_it0.991210592
X-RAY DIFFRACTIONr_scbond_it1.14533895
X-RAY DIFFRACTIONr_scangle_it1.9364.53319
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1978TIGHT POSITIONAL0.060.05
1A1978TIGHT THERMAL0.330.5
2B1978TIGHT POSITIONAL0.050.05
2B1978TIGHT THERMAL0.320.5
3C1903TIGHT POSITIONAL0.060.05
3C1903TIGHT THERMAL0.140.5
4D1978TIGHT POSITIONAL0.050.05
4D1978TIGHT THERMAL0.330.5
LS refinement shellResolution: 2.8→2.869 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 126 -
Rwork0.276 2205 -
obs-2331 99.74 %

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