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- PDB-5lc9: Structure of Polyphosphate Kinase from Meiothermus ruber Apo-form -

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Basic information

Entry
Database: PDB / ID: 5lc9
TitleStructure of Polyphosphate Kinase from Meiothermus ruber Apo-form
ComponentsPolyphosphate:AMP phosphotransferase
KeywordsTRANSFERASE / Polyphosphate Kinase
Function / homology
Function and homology information


phosphotransferase activity, phosphate group as acceptor / polyphosphate metabolic process / kinase activity
Similarity search - Function
Polyphosphate:nucleotide phosphotransferase, PPK2 / Polyphosphate phosphotransferase / Polyphosphate kinase-2-related / Polyphosphate kinase 2 (PPK2) / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Polyphosphate:AMP phosphotransferase
Similarity search - Component
Biological speciesMeiothermus ruber H328 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.903 Å
AuthorsKemper, F. / Einsle, O. / Gerhardt, S.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Substrate recognition and mechanism revealed by ligand-bound polyphosphate kinase 2 structures.
Authors: Parnell, A.E. / Mordhorst, S. / Kemper, F. / Giurrandino, M. / Prince, J.P. / Schwarzer, N.J. / Hofer, A. / Wohlwend, D. / Jessen, H.J. / Gerhardt, S. / Einsle, O. / Oyston, P.C.F. / Andexer, J.N. / Roach, P.L.
History
DepositionJun 20, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 11, 2018Group: Data collection / Database references / Source and taxonomy
Category: citation / entity_src_gen
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polyphosphate:AMP phosphotransferase
B: Polyphosphate:AMP phosphotransferase
C: Polyphosphate:AMP phosphotransferase
D: Polyphosphate:AMP phosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,87712
Polymers135,1134
Non-polymers7648
Water13,727762
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11210 Å2
ΔGint-137 kcal/mol
Surface area43890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.783, 164.783, 94.983
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
Polyphosphate:AMP phosphotransferase


Mass: 33778.340 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Meiothermus ruber H328 (bacteria) / Gene: MrH_2468 / Plasmid: pET28A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0S7ASE9
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 762 / 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: 2.64 Å3/Da / Density % sol: 53.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100mM TRIS/HCL pH 8.5 27%(w/v) PEG 3350 200mM Lithium sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 19, 2015 / Details: MIRROR
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.903→116.52 Å / Num. obs: 100534 / % possible obs: 100 % / Redundancy: 52.7 % / Biso Wilson estimate: 27.36 Å2 / Rmerge(I) obs: 0.247 / Rsym value: 0.247 / Net I/σ(I): 19.8
Reflection shellResolution: 1.903→2.01 Å / Redundancy: 46.7 % / Rmerge(I) obs: 2.931 / Mean I/σ(I) obs: 2.4 / % possible all: 100

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Processing

Software
NameVersionClassification
autoPROCdata reduction
Aimlessdata scaling
MOLREPphasing
BUSTER2.10.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RHF

3rhf


Resolution: 1.903→116.52 Å / Cor.coef. Fo:Fc: 0.9447 / Cor.coef. Fo:Fc free: 0.9275 / SU R Cruickshank DPI: 0.126 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.131 / SU Rfree Blow DPI: 0.113 / SU Rfree Cruickshank DPI: 0.111
RfactorNum. reflection% reflectionSelection details
Rfree0.1925 5064 4.95 %RANDOM
Rwork0.1721 ---
obs0.1731 100534 99.51 %-
Displacement parametersBiso mean: 37.14 Å2
Baniso -1Baniso -2Baniso -3
1--4.4512 Å20 Å20 Å2
2---4.4512 Å20 Å2
3---8.9023 Å2
Refine analyzeLuzzati coordinate error obs: 0.214 Å
Refinement stepCycle: LAST / Resolution: 1.903→116.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8687 0 40 762 9489
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018935HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9112098HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3268SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes260HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1293HARMONIC5
X-RAY DIFFRACTIONt_it8935HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.28
X-RAY DIFFRACTIONt_other_torsion16.69
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1049SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact10784SEMIHARMONIC4
LS refinement shellResolution: 1.903→1.95 Å
RfactorNum. reflection% reflection
Rfree0.2287 349 4.95 %
Rwork0.2122 6697 -
obs--93.86 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5349-0.09290.10450.6086-0.72032.4559-0.0293-0.0748-0.04760.0773-0.0351-0.03290.00620.1280.0644-0.02610.0321-0.0166-0.06610.0241-0.095956.5785-10.193226.5622
20.4950.0327-0.04920.9903-0.63781.3101-0.04410.08190.03480.132-0.0063-0.054-0.21450.10540.0504-0.0289-0.0059-0.0088-0.0330.0189-0.082156.791710.1064-6.1557
31.1519-0.0034-0.11890.74240.33791.2007-0.00810.3489-0.0601-0.0108-0.03430.04910.1155-0.14620.0424-0.11340.0199-0.02280.0461-0.0177-0.097327.3137-6.029-9.1354
41.44290.0840.62020.62090.0252.2211-0.1167-0.41130.13190.1494-0.0280.109-0.2221-0.30110.1448-0.08290.05050.0192-0.0021-0.0484-0.135725.59613.719828.137
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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