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

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Basic information

Entry
Database: PDB / ID: 4fwp
TitleCrystal structure of Salmonella typhimurium propionate kinase (TdcD) in complex with GDP
ComponentsPropionate kinase
KeywordsTRANSFERASE / Kinase / Acetate and Sugar Kinases/Hsc70/Actin (ASKHA) superfamily / TdcD / GDP / 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'-DIPHOSPHATE / Propionate kinase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 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)45,8144
Polymers45,2461
Non-polymers5673
Water1,20767
1
A: Propionate kinase
hetero molecules

A: Propionate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,6278
Polymers90,4932
Non-polymers1,1356
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area8420 Å2
ΔGint-38 kcal/mol
Surface area29080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.489, 111.489, 66.888
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-632-

HOH

21A-634-

HOH

31A-647-

HOH

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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.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.65 Å3/Da / Density % sol: 53.62 % / Mosaicity: 1.283 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Bis-Tris pH 6.5, 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 20, 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: 2.5→50 Å / Num. obs: 16944 / % possible obs: 99.8 % / Redundancy: 15.7 % / Rmerge(I) obs: 0.088 / Χ2: 1.031 / Net I/σ(I): 19.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.5-2.5912.90.47116821.277199.9
2.59-2.6914.80.40216511.3421100
2.69-2.8215.20.31516871.3681100
2.82-2.9615.40.2516741.4491100
2.96-3.1515.60.18416791.381199.9
3.15-3.3915.90.13816801.205199.9
3.39-3.7316.30.10117021199.8
3.73-4.2716.80.07616930.765199.6
4.27-5.3817.10.05917050.486199.1
5.38-5017.30.06617910.337199.6

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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
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2E1Y

2e1y


Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.908 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 9.609 / SU ML: 0.218 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.528 / ESU R Free: 0.294 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2661 857 5.1 %RANDOM
Rwork0.2354 ---
obs0.2369 16917 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 96.27 Å2 / Biso mean: 54.7753 Å2 / Biso min: 19.39 Å2
Baniso -1Baniso -2Baniso -3
1-2.51 Å21.25 Å20 Å2
2--2.51 Å20 Å2
3----3.76 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2926 0 36 67 3029
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0213024
X-RAY DIFFRACTIONr_angle_refined_deg0.9221.9614114
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6075395
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.75723.6125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.96115469
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8811520
X-RAY DIFFRACTIONr_chiral_restr0.060.2480
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212275
X-RAY DIFFRACTIONr_mcbond_it0.2861.51949
X-RAY DIFFRACTIONr_mcangle_it0.52623106
X-RAY DIFFRACTIONr_scbond_it0.48231075
X-RAY DIFFRACTIONr_scangle_it0.8724.51007
LS refinement shellResolution: 2.496→2.561 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.424 73 -
Rwork0.302 1148 -
all-1221 -
obs--98.95 %

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