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- PDB-7fj7: KpAckA (PduW) native structure -

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Basic information

Entry
Database: PDB / ID: 7fj7
TitleKpAckA (PduW) native 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 / acetate kinase activity / acetate metabolic process / 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
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWu, W. / Zhang, Q. / Bartlam, M.
Funding support2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31800627
National Natural Science Foundation of China (NSFC)31870053
CitationJournal: To Be Published
Title: KpAckA (PduW) native 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


Theoretical massNumber of molelcules
Total (without water)87,3322
Polymers87,3322
Non-polymers00
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5950 Å2
ΔGint-56 kcal/mol
Surface area29780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.865, 101.510, 90.794
Angle α, β, γ (deg.)90.000, 125.189, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 3.27 Å3/Da / Density % sol: 62.44 %
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: Mar 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 38499 / % possible obs: 98.8 % / Redundancy: 6.8 % / Biso Wilson estimate: 34.27 Å2 / Rpim(I) all: 0.032 / Net I/σ(I): 21.45
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 3.5 / Num. unique obs: 1895 / Rpim(I) all: 0.211 / % possible all: 97.2

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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: 2IIR

2iir


Resolution: 2.5→45.38 Å / SU ML: 0.296 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.1712
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2301 1985 5.42 %
Rwork0.1808 34662 -
obs0.1835 36647 93.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.88 Å2
Refinement stepCycle: LAST / Resolution: 2.5→45.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5945 0 0 19 5964
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00776047
X-RAY DIFFRACTIONf_angle_d0.93888189
X-RAY DIFFRACTIONf_chiral_restr0.0508941
X-RAY DIFFRACTIONf_plane_restr0.00551067
X-RAY DIFFRACTIONf_dihedral_angle_d8.837842
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.560.2891110.20871848X-RAY DIFFRACTION70.59
2.56-2.630.26081240.20112096X-RAY DIFFRACTION80.2
2.63-2.710.291210.21582261X-RAY DIFFRACTION85.84
2.71-2.80.29271400.21262390X-RAY DIFFRACTION91.14
2.8-2.90.29981460.22282578X-RAY DIFFRACTION97.46
2.9-3.010.29011530.21722590X-RAY DIFFRACTION99.38
3.01-3.150.26791470.21782626X-RAY DIFFRACTION99.53
3.15-3.320.26881480.20522534X-RAY DIFFRACTION96.41
3.32-3.520.24691420.1952616X-RAY DIFFRACTION99.6
3.52-3.80.21011520.17452647X-RAY DIFFRACTION99.79
3.8-4.180.21271520.15922616X-RAY DIFFRACTION99.86
4.18-4.780.18861490.13972592X-RAY DIFFRACTION97.82
4.78-6.020.21441500.16472642X-RAY DIFFRACTION99.47
6.02-45.380.1691500.16072626X-RAY DIFFRACTION96.96
Refinement TLS params.Method: refined / Origin x: 29.374470653 Å / Origin y: 29.5826258628 Å / Origin z: 22.0284106591 Å
111213212223313233
T0.219335688492 Å20.0336149691331 Å2-0.0287532459321 Å2-0.196773540464 Å20.0143879023457 Å2--0.145388423699 Å2
L1.19047043899 °20.359937899544 °2-0.194734719386 °2-0.737961743635 °2-0.150991053414 °2--0.309948339751 °2
S0.0601143124813 Å °0.275932734602 Å °0.10797754368 Å °-0.207139549717 Å °-0.0532675782637 Å °0.131684137859 Å °0.117749880326 Å °-0.0781181952312 Å °0.00862860016869 Å °
Refinement TLS groupSelection details: all

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