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- PDB-2e1z: Crystal structure of Salmonella typhimurium propionate kinase (Td... -

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Basic information

Entry
Database: PDB / ID: 2e1z
TitleCrystal structure of Salmonella typhimurium propionate kinase (TdcD) in complex with diadenosine tetraphosphate (Ap4A) obtained after co-crystallization with ATP
ComponentsPropionate Kinase
KeywordsTRANSFERASE / Propionate kinase / TdcD / Native / Acetate kinase / Nucleotide / Ap4A / ADP / ATP / AMPPNP
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
BIS(ADENOSINE)-5'-TETRAPHOSPHATE / Propionate kinase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.98 Å
AuthorsSimanshu, D.K. / Savithri, H.S. / Murthy, M.R.N.
Citation
Journal: Proteins / Year: 2008
Title: Crystal structures of Salmonella typhimurium propionate kinase and its complex with Ap4A: evidence for a novel Ap4A synthetic activity.
Authors: Simanshu, D.K. / Savithri, H.S. / Murthy, M.R.N.
#1: Journal: J.Mol.Biol. / Year: 2005
Title: Crystal structures of ADP and AMPPNP-bound propionate kinase (TdcD) from Salmonella typhimurium: comparison with members of acetate and sugar kinase/heat shock cognate 70/actin superfamily
Authors: Simanshu, D.K. / Savithri, H.S. / Murthy, M.R.
#2: Journal: ACTA CRYSTALLOGR.,SECT.F / Year: 2005
Title: Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of propionate kinase (TdcD) from Salmonella typhimurium
Authors: Simanshu, D.K. / Murthy, M.R.
History
DepositionNov 4, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software
Revision 1.3Oct 25, 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)46,1453
Polymers45,2461
Non-polymers8982
Water3,405189
1
A: Propionate Kinase
hetero molecules

A: Propionate Kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,2906
Polymers90,4932
Non-polymers1,7974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area9380 Å2
ΔGint-41 kcal/mol
Surface area28240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.483, 110.483, 66.607
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-491-

HOH

21A-514-

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: IFO 12529 / Gene: TdcD / Plasmid: pRSET C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: O06961, propionate kinase
#2: Chemical ChemComp-B4P / BIS(ADENOSINE)-5'-TETRAPHOSPHATE


Mass: 836.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28N10O19P4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 2.59 Å3/Da / Density % sol: 52.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Bis-Tris pH 6.5, 17% (w/v) polyethylene glycol monomethyl ether 5000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Dec 7, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. obs: 32959 / % possible obs: 99.9 % / Redundancy: 13.88 % / Biso Wilson estimate: 45.2 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 24.41
Reflection shellResolution: 1.98→2.05 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 2.19 / Num. unique all: 3248 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1X3M

1x3m


Resolution: 1.98→30 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.711 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22092 1596 5.1 %RANDOM
Rwork0.19055 ---
obs0.19207 29989 95.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.577 Å2
Baniso -1Baniso -2Baniso -3
1-1.61 Å20.81 Å20 Å2
2--1.61 Å20 Å2
3----2.42 Å2
Refinement stepCycle: LAST / Resolution: 1.98→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2955 0 57 189 3201
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0213070
X-RAY DIFFRACTIONr_bond_other_d0.0010.021978
X-RAY DIFFRACTIONr_angle_refined_deg1.1771.9754183
X-RAY DIFFRACTIONr_angle_other_deg0.8934823
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6955397
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.49723.566129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.61715480
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9821522
X-RAY DIFFRACTIONr_chiral_restr0.0690.2486
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023457
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02620
X-RAY DIFFRACTIONr_nbd_refined0.1980.2636
X-RAY DIFFRACTIONr_nbd_other0.1890.22143
X-RAY DIFFRACTIONr_nbtor_refined0.1690.21508
X-RAY DIFFRACTIONr_nbtor_other0.0820.21634
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2161
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2280.275
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.120.214
X-RAY DIFFRACTIONr_mcbond_it0.6391.52001
X-RAY DIFFRACTIONr_mcbond_other0.11.5813
X-RAY DIFFRACTIONr_mcangle_it1.07723110
X-RAY DIFFRACTIONr_scbond_it1.42531200
X-RAY DIFFRACTIONr_scangle_it2.354.51071
LS refinement shellResolution: 1.98→2.031 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 114 -
Rwork0.247 1985 -
obs--87.93 %

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