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- PDB-7fj9: KpAckA (PduW) with AMPPNP complex structure -

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Basic information

Entry
Database: PDB / ID: 7fj9
TitleKpAckA (PduW) with AMPPNP complex structure
ComponentsProbable propionate kinase
KeywordsTRANSFERASE / Acetate utilization pathway / Acetate kinase / Klebsiella pneumoniae
Function / homology
Function and homology information


propionate kinase / propanediol catabolic process / propionate kinase activity / propionate catabolic process / phosphorylation / 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
ACETATE ION / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Propionate kinase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)88,4626
Polymers87,3322
Non-polymers1,1304
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6330 Å2
ΔGint-59 kcal/mol
Surface area29390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.558, 153.701, 131.154
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-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.93 Å3/Da / Density % sol: 58.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 0.2 M Ammonium citrate tribasic, 20% Polyethylene glycol 3350, pH 7.0

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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: Apr 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 46221 / % possible obs: 99.9 % / Redundancy: 6.3 % / Biso Wilson estimate: 37.15 Å2 / Rpim(I) all: 0.057 / Net I/σ(I): 11.15
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 1.15 / Num. unique obs: 2266 / Rpim(I) all: 0.472 / % possible all: 99.7

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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: 2.3→42.37 Å / SU ML: 0.308 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.1514
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2381 2000 4.33 %
Rwork0.1925 44166 -
obs0.1945 46166 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.8 Å2
Refinement stepCycle: LAST / Resolution: 2.3→42.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5728 0 70 18 5816
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00825894
X-RAY DIFFRACTIONf_angle_d0.91797992
X-RAY DIFFRACTIONf_chiral_restr0.0505924
X-RAY DIFFRACTIONf_plane_restr0.0051028
X-RAY DIFFRACTIONf_dihedral_angle_d14.2198831
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.350.32371310.27692903X-RAY DIFFRACTION92.53
2.35-2.410.31811420.26383137X-RAY DIFFRACTION99.94
2.41-2.480.34421420.24783133X-RAY DIFFRACTION99.85
2.48-2.560.31971420.22813130X-RAY DIFFRACTION99.94
2.56-2.650.2661430.2193153X-RAY DIFFRACTION100
2.65-2.760.29651420.21513139X-RAY DIFFRACTION99.91
2.76-2.890.25571430.21813152X-RAY DIFFRACTION100
2.89-3.040.25751420.21923148X-RAY DIFFRACTION100
3.04-3.230.29031440.21443170X-RAY DIFFRACTION100
3.23-3.480.2531430.19483169X-RAY DIFFRACTION100
3.48-3.830.20991450.17653188X-RAY DIFFRACTION99.97
3.83-4.380.20981440.15183201X-RAY DIFFRACTION100
4.38-5.520.1631470.1523229X-RAY DIFFRACTION99.97
5.52-42.370.21651500.1873314X-RAY DIFFRACTION99.34
Refinement TLS params.Method: refined / Origin x: 16.3209050306 Å / Origin y: 21.7725219967 Å / Origin z: -13.9814106119 Å
111213212223313233
T0.241587902319 Å2-0.0438889990024 Å20.00723865335939 Å2-0.248057888967 Å20.0219801800062 Å2--0.231413348132 Å2
L0.905449897778 °2-0.316495284477 °20.0401178412906 °2-1.54259290906 °20.128178294399 °2--0.499834406697 °2
S-0.0179072915625 Å °0.180776075971 Å °0.0501128667427 Å °-0.259978472878 Å °0.0249676153267 Å °-0.116575593202 Å °0.00287592841331 Å °-0.0656930654541 Å °-0.00663350222002 Å °
Refinement TLS groupSelection details: all

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