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- PDB-1tz6: Crystal structure of aminoimidazole riboside kinase from Salmonel... -

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Basic information

Entry
Database: PDB / ID: 1tz6
TitleCrystal structure of aminoimidazole riboside kinase from Salmonella enterica complexed with aminoimidazole riboside and ATP analog
Componentsputative sugar kinase
KeywordsTRANSFERASE / ribokinase fold / alpha/beta
Function / homology
Function and homology information


aminoimidazole riboside kinase / fructokinase activity / fructose metabolic process / ATP binding / metal ion binding
Similarity search - Function
Ribokinase/fructokinase / pfkB family of carbohydrate kinases signature 2. / Carbohydrate/purine kinase, PfkB, conserved site / Carbohydrate kinase PfkB / pfkB family carbohydrate 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 / 5-AMINOIMIDAZOLE RIBONUCLEOSIDE / : / Aminoimidazole riboside kinase
Similarity search - Component
Biological speciesSalmonella typhimurium LT2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsZhang, Y. / Dougherty, M. / Downs, D.M. / Ealick, S.E.
CitationJournal: STRUCTURE / Year: 2004
Title: Crystal Structure of an Aminoimidazole Riboside Kinase from Salmonella enterica; Implications for the Evolution of the Ribokinase Superfamily
Authors: Zhang, Y. / Dougherty, M. / Downs, D.M. / Ealick, S.E.
History
DepositionJul 9, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: putative sugar kinase
B: putative sugar kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,30911
Polymers72,8782
Non-polymers1,4319
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-25 kcal/mol
Surface area23100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.007, 54.101, 89.895
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein putative sugar kinase


Mass: 36439.082 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium LT2 (bacteria)
Species: Salmonella typhimuriumSalmonella enterica subsp. enterica
Strain: CT18 / Gene: Stm4066 / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)pLysS / References: UniProt: Q8ZKR2, fructokinase

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Non-polymers , 5 types, 66 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-AIS / 5-AMINOIMIDAZOLE RIBONUCLEOSIDE


Mass: 215.207 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H13N3O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.4 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: PEG3350, potassium sulfate, tertiary-butanol or isopropanol, DTT, MES, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 21, 2003
RadiationMonochromator: Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 18879 / Num. obs: 18879 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 44.1 Å2 / Rsym value: 0.049 / Net I/σ(I): 23.1
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 4.5 / Num. unique all: 1854 / Rsym value: 0.295 / % possible all: 99.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TYY

1tyy


Resolution: 2.7→37.58 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 166577.38 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.285 1781 9.9 %RANDOM
Rwork0.217 ---
all0.227 18076 --
obs0.217 18076 95 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.1858 Å2 / ksol: 0.318744 e/Å3
Displacement parametersBiso mean: 51.7 Å2
Baniso -1Baniso -2Baniso -3
1-13.73 Å20 Å20 Å2
2--7.46 Å20 Å2
3----21.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.59 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.7→37.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4443 0 83 57 4583
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.96
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.409 278 10.1 %
Rwork0.33 2478 -
obs--88.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3AIRS-PRODRG.PARAMAIRS-PRODRG.TOP
X-RAY DIFFRACTION4ACP-PRODRG.PARAMACP-PRODRG.TOP
X-RAY DIFFRACTION5ION.PARAMION.TOP

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