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- PDB-4xh5: Crystal structure of Salmonella typhimurium propionate kinase A88... -

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Basic information

Entry
Database: PDB / ID: 4xh5
TitleCrystal structure of Salmonella typhimurium propionate kinase A88G mutant, in complex with AMPPNP and propionate
ComponentsPropionate kinase
KeywordsTRANSFERASE / KINASE / TDCD mutant / AMPPNP / PROPIONATE
Function / homology
Function and homology information


propionate kinase / propionate kinase activity / : / 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: 2.11 Å
AuthorsMurthy, A.M. / Mathivanan, S. / Chittori, S. / Savithri, H.S. / Murthy, M.R.N.
Funding support India, 1items
OrganizationGrant numberCountry
DBT 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 1.0Sep 23, 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

Downloads & links

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Assembly

Deposited unit
A: Propionate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6045
Polymers44,8361
Non-polymers7684
Water1,892105
1
A: Propionate kinase
hetero molecules

A: Propionate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,20910
Polymers89,6722
Non-polymers1,5378
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area8980 Å2
ΔGint-53 kcal/mol
Surface area28480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.000, 111.000, 66.440
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-402-

GOL

21A-402-

GOL

31A-561-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Propionate kinase


Mass: 44835.938 Da / Num. of mol.: 1 / Fragment: UNP residues 4-397 / Mutation: A88G
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

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Non-polymers , 5 types, 109 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#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: Chemical ChemComp-PPI / PROPANOIC ACID


Mass: 74.079 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.52 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Bis-Tris pH 6.5, 30% pentaerythritol ethoxylate, 0.05M ammonium sulphate

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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: Feb 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: 2.11→42.59 Å / Num. obs: 27037 / % possible obs: 99 % / Redundancy: 5.5 % / Rsym value: 0.1 / Net I/σ(I): 9.5
Reflection shellResolution: 2.11→2.23 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 3.2 / % possible all: 95.9

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Processing

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

2e1y


Resolution: 2.11→42.59 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.93 / SU B: 4.745 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.18 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23068 1359 5 %RANDOM
Rwork0.17468 ---
obs0.17746 25673 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: 37.994 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.11→42.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2917 0 47 105 3069
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0193014
X-RAY DIFFRACTIONr_bond_other_d0.0020.022834
X-RAY DIFFRACTIONr_angle_refined_deg1.8561.9654097
X-RAY DIFFRACTIONr_angle_other_deg0.88436468
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6035388
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.10523.492126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.37715464
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5551521
X-RAY DIFFRACTIONr_chiral_restr0.1050.2478
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023441
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02693
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_it3.1113.7691563
X-RAY DIFFRACTIONr_mcbond_other3.1113.7671562
X-RAY DIFFRACTIONr_mcangle_it4.2765.6211948
X-RAY DIFFRACTIONr_mcangle_other4.2755.6231949
X-RAY DIFFRACTIONr_scbond_it4.0244.0321451
X-RAY DIFFRACTIONr_scbond_other4.0224.0331452
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6565.9592150
X-RAY DIFFRACTIONr_long_range_B_refined7.12930.4513405
X-RAY DIFFRACTIONr_long_range_B_other7.12630.4523405
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.113→2.168 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 84 -
Rwork0.245 1757 -
obs--91.82 %

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