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- PDB-4fwo: Crystal structure of Salmonella typhimurium propionate kinase (Td... -

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Basic information

Entry
Database: PDB / ID: 4fwo
TitleCrystal structure of Salmonella typhimurium propionate kinase (TdcD) in complex with GMP
ComponentsPropionate kinase
KeywordsTRANSFERASE / Kinase / Acetate and Sugar Kinases/Hsc70/Actin (ASKHA) superfamily / Propionate kinase / TdcD / GMP / Short-Chain Fatty Acid
Function / homology
Function and homology information


propionate kinase / propionate kinase activity / L-threonine catabolic process to propionate / acetate kinase activity / acetate metabolic process / ATP binding / metal ion binding / cytosol
Similarity search - Function
Propionate kinase / Acetate and butyrate kinases family signature 2. / Acetate/propionate kinase / Aliphatic acid kinase, short-chain, conserved site / Acetate and butyrate kinases family signature 1. / Aliphatic acid kinase, short-chain / Acetokinase family / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 ...Propionate kinase / Acetate and butyrate kinases family signature 2. / Acetate/propionate kinase / Aliphatic acid kinase, short-chain, conserved site / Acetate and butyrate kinases family signature 1. / Aliphatic acid kinase, short-chain / Acetokinase family / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-MONOPHOSPHATE / Propionate kinase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å
AuthorsChittori, S. / Savithri, H.S. / Murthy, M.R.N.
CitationJournal: Biochim.Biophys.Acta / Year: 2013
Title: Mechanistic features of Salmonella typhimurium propionate kinase (TdcD): insights from kinetic and crystallographic studies.
Authors: Chittori, S. / Simanshu, D.K. / Banerjee, S. / Murthy, A.M.V. / Mathivanan, S. / Savithri, H.S. / Murthy, M.R.N.
History
DepositionJul 1, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Nov 8, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Propionate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7965
Polymers45,2461
Non-polymers5494
Water1,11762
1
A: Propionate kinase
hetero molecules

A: Propionate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,59210
Polymers90,4932
Non-polymers1,0998
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area8440 Å2
ΔGint-38 kcal/mol
Surface area29760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.921, 110.921, 66.789
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Propionate kinase


Mass: 45246.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: oxd-2, STM3242, tdcD / Plasmid: pRSET C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O06961, propionate kinase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O8P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.62 Å3/Da / Density % sol: 53.08 % / Mosaicity: 2.506 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M Bis-Tris pH 6.0, 35% Pentaerythritol ethoxylate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 4, 2008 / Details: Mirror
RadiationMonochromator: Osmic Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 10515 / % possible obs: 97.6 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.142 / Χ2: 1.006 / Net I/σ(I): 62.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.9-33.70.30710312.39196.7
3-3.123.90.28210012.045197
3.12-3.2740.25510471.856197.6
3.27-3.444.20.22410261.453197.4
3.44-3.654.20.19910351.133196.8
3.65-3.944.10.17510600.896198
3.94-4.3340.15110280.75195.9
4.33-4.964.40.12310590.516197.9
4.96-6.246.20.12410800.431199.5
6.24-507.40.10711480.285199.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0072refinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2E1Y

2e1y


Resolution: 2.9→50 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.857 / Occupancy max: 1 / Occupancy min: 1 / SU B: 18.77 / SU ML: 0.366 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.471 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2871 501 4.8 %RANDOM
Rwork0.2281 ---
obs0.2308 10512 97.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 85.93 Å2 / Biso mean: 44.3506 Å2 / Biso min: 3.53 Å2
Baniso -1Baniso -2Baniso -3
1-2.92 Å21.46 Å20 Å2
2--2.92 Å20 Å2
3----4.38 Å2
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2949 0 36 62 3047
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0213038
X-RAY DIFFRACTIONr_angle_refined_deg0.9551.9624123
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6475393
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.4923.465127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.24315483
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3251522
X-RAY DIFFRACTIONr_chiral_restr0.060.2480
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212279
X-RAY DIFFRACTIONr_mcbond_it0.2621.51946
X-RAY DIFFRACTIONr_mcangle_it0.47623105
X-RAY DIFFRACTIONr_scbond_it0.38431092
X-RAY DIFFRACTIONr_scangle_it0.6544.51018
LS refinement shellResolution: 2.901→2.976 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.408 37 -
Rwork0.28 688 -
all-725 -
obs--95.02 %

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