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- PDB-4xh1: Crystal structure of Salmonella typhimurium propionate kinase in ... -

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Basic information

Entry
Database: PDB / ID: 4xh1
TitleCrystal structure of Salmonella typhimurium propionate kinase in complex with AMPPNP and propionate
ComponentsPropionate kinase
KeywordsTRANSFERASE / KINASE / TDCD / AMPPNP / PROPIONATE
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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / PROPANOIC ACID / Propionate kinase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMurthy, A.M.V. / Mathivanan, S. / Chittori, S. / Savithri, H.S. / Murthy, M.R.N.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology India
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structures of substrate- and nucleotide-bound propionate kinase from Salmonella typhimurium: substrate specificity and phosphate-transfer mechanism
Authors: Murthy, A.M.V. / Mathivanan, S. / Chittori, S. / Savithri, H.S. / Murthy, M.R.N.
History
DepositionJan 4, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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)46,1425
Polymers45,3781
Non-polymers7644
Water2,018112
1
A: Propionate kinase
hetero molecules

A: Propionate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,28410
Polymers90,7552
Non-polymers1,5298
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_676x-y+1,-y+2,-z+5/31
Buried area9060 Å2
ΔGint-35 kcal/mol
Surface area28740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.610, 111.610, 66.650
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-645-

HOH

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Components

#1: Protein Propionate kinase


Mass: 45377.590 Da / Num. of mol.: 1 / Fragment: UNP residues 4-397 / Mutation: Q381E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: tdcD, oxd-2, STM3242 / Plasmid: PRSET C PRSET C PRSETPRSET PRSET C / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O06961, propionate kinase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PPI / PROPANOIC ACID


Mass: 74.079 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O2
#4: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.8 Å3/Da / Density % sol: 56.02 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M Bis-Tris pH 6.5, polyethylene glycol 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.976 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 22, 2014
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2→32.22 Å / Num. obs: 32233 / % possible obs: 99 % / Observed criterion σ(F): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 31.469 Å2 / Rsym value: 0.071 / Net I/σ(I): 17
Reflection shellResolution: 2→2.11 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 4 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
SCALAdata scaling
PHASERphasing
Cootmodel building
iMOSFLM1.0.7data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2E1Y

2e1y


Resolution: 2→32.22 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.483 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22615 1634 5.1 %RANDOM
Rwork0.17995 ---
obs0.18227 30589 98.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.912 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→32.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2923 0 48 112 3083
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193021
X-RAY DIFFRACTIONr_bond_other_d0.0010.022861
X-RAY DIFFRACTIONr_angle_refined_deg1.9531.9674104
X-RAY DIFFRACTIONr_angle_other_deg0.90936531
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6775391
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.66723.415123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.61315470
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.411521
X-RAY DIFFRACTIONr_chiral_restr0.1160.2481
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023441
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02691
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.3753.3621569
X-RAY DIFFRACTIONr_mcbond_other3.3683.361568
X-RAY DIFFRACTIONr_mcangle_it4.5335.0141957
X-RAY DIFFRACTIONr_mcangle_other4.5335.0161958
X-RAY DIFFRACTIONr_scbond_it4.1293.7441452
X-RAY DIFFRACTIONr_scbond_other4.1283.7451453
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0065.4822148
X-RAY DIFFRACTIONr_long_range_B_refined7.42427.6463411
X-RAY DIFFRACTIONr_long_range_B_other7.42327.6513412
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 116 -
Rwork0.213 2198 -
obs--98.38 %

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