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

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Basic information

Entry
Database: PDB / ID: 4fwm
TitleCrystal structure of Salmonella typhimurium propionate kinase (TdcD) in complex with ATP
ComponentsPropionate kinase
KeywordsTRANSFERASE / Kinase / Acetate and Sugar Kinases/Hsc70/Actin (ASKHA) superfamily / Propionate kinase / TdcD / 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 / phosphorylation / 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
ADENOSINE-5'-TRIPHOSPHATE / Propionate kinase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.95 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
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
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)45,4586
Polymers44,7031
Non-polymers7555
Water50428
1
A: Propionate kinase
hetero molecules

A: Propionate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,91612
Polymers89,4062
Non-polymers1,51110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area8330 Å2
ΔGint-35 kcal/mol
Surface area29640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.435, 111.435, 66.753
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: 44702.793 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 / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.68 Å3/Da / Density % sol: 54.04 % / Mosaicity: 1.389 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M Bis-Tris pH 6.0, 30% hexanediol, 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: Nov 29, 2009 / 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: 2.95→50 Å / Num. obs: 10303 / % possible obs: 99.2 % / Redundancy: 8 % / Rmerge(I) obs: 0.064 / Χ2: 0.686 / Net I/σ(I): 19.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.95-3.066.40.5199971.113197.7
3.06-3.186.70.37510101.024198.9
3.18-3.327.20.23910030.962199.4
3.32-3.57.50.17210140.951199
3.5-3.727.80.11410460.858199
3.72-48.30.0899970.822199.7
4-4.4190.06310400.66199.7
4.41-5.049.20.04810330.348199.7
5.04-6.359.10.04810530.324199.8
6.35-508.70.02811100.245199.3

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Processing

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

2e1y


Resolution: 2.95→50 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.889 / Occupancy max: 1 / Occupancy min: 1 / SU B: 18.811 / SU ML: 0.357 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.482 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2909 495 4.8 %RANDOM
Rwork0.234 ---
obs0.2366 10287 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 107.31 Å2 / Biso mean: 63.6581 Å2 / Biso min: 36.25 Å2
Baniso -1Baniso -2Baniso -3
1-1.93 Å20.96 Å20 Å2
2--1.93 Å20 Å2
3----2.89 Å2
Refinement stepCycle: LAST / Resolution: 2.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2897 0 47 28 2972
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0212994
X-RAY DIFFRACTIONr_angle_refined_deg0.9871.9614072
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7355393
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.88223.577123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.71415445
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1841520
X-RAY DIFFRACTIONr_chiral_restr0.0650.2474
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212257
X-RAY DIFFRACTIONr_mcbond_it0.3461.51942
X-RAY DIFFRACTIONr_mcangle_it0.63423085
X-RAY DIFFRACTIONr_scbond_it0.51431052
X-RAY DIFFRACTIONr_scangle_it0.944.5987
LS refinement shellResolution: 2.946→3.022 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 37 -
Rwork0.322 699 -
all-736 -
obs--96.71 %

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