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- PDB-7fja: KpAckA (PduW) with AMPPNP, ethylene glycol complex structure -

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Basic information

Entry
Database: PDB / ID: 7fja
TitleKpAckA (PduW) with AMPPNP, ethylene glycol complex structure
ComponentsProbable propionate kinase
KeywordsTRANSFERASE / Acetate utilization pathway / Acetate kinase / Klebsiella pneumoniae
Function / homology
Function and homology information


propionate kinase / propionate kinase activity / propanediol catabolic process / propionate catabolic process / ATP binding / cytoplasm
Similarity search - Function
Propionate kinase PduW / 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
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Propionate kinase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWu, W. / Zhang, Q. / Bartlam, M.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31800627 China
National Natural Science Foundation of China (NSFC)31870053 China
CitationJournal: To Be Published
Title: KpAckA (PduW) with AMPPNP, ethylene glycol complex structure
Authors: Wu, W. / Zhang, Q. / Bartlam, M.
History
DepositionAug 3, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable propionate kinase
B: Probable propionate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,4065
Polymers87,3322
Non-polymers1,0743
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5870 Å2
ΔGint-55 kcal/mol
Surface area28380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.097, 152.187, 131.738
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Probable propionate kinase


Mass: 43666.004 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3GUQ7, propionate kinase
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.96 Å3/Da / Density % sol: 58.42 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 0.1 M BIS-TRIS, 45% v/v Polypropylene glycol P 400, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 53723 / % possible obs: 100 % / Redundancy: 8 % / Biso Wilson estimate: 26.6 Å2 / Rpim(I) all: 0.047 / Net I/σ(I): 15.92
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 4.45 / Num. unique obs: 2641 / Rpim(I) all: 0.325 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7FJ7

7fj7


Resolution: 2.2→43.02 Å / SU ML: 0.2097 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.8361
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2301 2960 3.74 %
Rwork0.1945 76192 -
obs0.1958 53446 75.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.69 Å2
Refinement stepCycle: LAST / Resolution: 2.2→43.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5437 0 66 82 5585
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00785598
X-RAY DIFFRACTIONf_angle_d0.92817586
X-RAY DIFFRACTIONf_chiral_restr0.0543868
X-RAY DIFFRACTIONf_plane_restr0.005975
X-RAY DIFFRACTIONf_dihedral_angle_d14.2167790
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.220.2676760.22671954X-RAY DIFFRACTION40.98
2.22-2.260.2525930.232403X-RAY DIFFRACTION50.33
2.26-2.30.2649950.22052456X-RAY DIFFRACTION51.01
2.3-2.340.2582950.22362468X-RAY DIFFRACTION52.17
2.34-2.390.25281020.21892591X-RAY DIFFRACTION54.2
2.39-2.440.24891070.21412758X-RAY DIFFRACTION57.69
2.44-2.50.25151210.21013012X-RAY DIFFRACTION62.94
2.5-2.560.20311250.2083232X-RAY DIFFRACTION67.5
2.56-2.630.21631330.21493497X-RAY DIFFRACTION72.6
2.63-2.710.2571400.22033710X-RAY DIFFRACTION77.87
2.71-2.790.25761420.21693937X-RAY DIFFRACTION82.19
2.79-2.890.29331670.21844091X-RAY DIFFRACTION86.16
2.89-3.010.28181740.21114419X-RAY DIFFRACTION92.94
3.01-3.150.20721700.21564499X-RAY DIFFRACTION92.88
3.15-3.310.27251670.2124431X-RAY DIFFRACTION92.98
3.31-3.520.22471650.19474313X-RAY DIFFRACTION90.3
3.52-3.790.21821670.18034215X-RAY DIFFRACTION88.2
3.79-4.170.21521740.16734442X-RAY DIFFRACTION93.05
4.17-4.770.21061740.15344433X-RAY DIFFRACTION92.85
4.77-6.010.211860.1734662X-RAY DIFFRACTION97.66
6.02-43.020.20241870.20164669X-RAY DIFFRACTION97.43
Refinement TLS params.Method: refined / Origin x: 15.7531099039 Å / Origin y: 22.8762267904 Å / Origin z: -12.3774682607 Å
111213212223313233
T0.19884646214 Å2-0.0546218087091 Å20.00105866488923 Å2-0.236200803419 Å20.00679845592141 Å2--0.10191391873 Å2
L0.835996328184 °2-0.348907775014 °2-0.0581008861611 °2-3.15467921538 °20.247204426926 °2--0.471800058318 °2
S-0.088909997115 Å °0.142019644993 Å °0.0894323316941 Å °-0.589962519391 Å °0.107685883308 Å °-0.122386592052 Å °-0.0693001228284 Å °-0.102712676946 Å °-0.0117961958739 Å °
Refinement TLS groupSelection details: all

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