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- PDB-5lcd: Structure of Polyphosphate Kinase from Meiothermus ruber bound to AMP -

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Basic information

Entry
Database: PDB / ID: 5lcd
TitleStructure of Polyphosphate Kinase from Meiothermus ruber bound to AMP
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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / PHOSPHATE ION / Polyphosphate:AMP phosphotransferase
Similarity search - Component
Biological speciesMeiothermus ruber H328 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.66 Å
AuthorsGerhardt, S. / Einsle, O. / Kemper, F. / Schwarzer, N.
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 21, 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 / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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

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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)137,86723
Polymers135,1134
Non-polymers2,75419
Water1,36976
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14980 Å2
ΔGint-212 kcal/mol
Surface area43600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.441, 164.441, 95.044
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Polyphosphate:AMP phosphotransferase


Mass: 33778.340 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: the residues Met -19 to His 0 have been introduced by the expression tag of pET28A MET 1 in chains A,B,C and D is the initiating methionine
Source: (gene. exp.) Meiothermus ruber H328 (bacteria) / Gene: MrH_2468 / Plasmid: pET28A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0S7ASE9

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Non-polymers , 5 types, 95 molecules

#2: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


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


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.62 Å3/Da / Density % sol: 53.08 % / Mosaicity: 0.53 °
Crystal growTemperature: 298 K / Method: evaporation / pH: 8.5 / Details: PEG3350, Li2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00001 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 28, 2015 / Details: MIRROR
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 2.66→116.28 Å / Num. obs: 37790 / % possible obs: 99.6 % / Redundancy: 44 % / Biso Wilson estimate: 54.44 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.322 / Rpim(I) all: 0.049 / Rrim(I) all: 0.329 / Rsym value: 0.33 / Net I/σ(I): 17.3 / Num. measured all: 1661253 / Scaling rejects: 14
Reflection shellResolution: 2.66→2.68 Å / Redundancy: 31.2 % / Rmerge(I) obs: 2.089 / Mean I/σ(I) obs: 2.4 / % possible all: 99.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.5.14data scaling
MOLREPphasing
BUSTER-TNT2.10.3refinement
PDB_EXTRACT3.2data extraction
autoPROC1.0.5data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LC9

5lc9


Resolution: 2.66→116.28 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.885 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 1.089 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.069 / SU Rfree Blow DPI: 0.32 / SU Rfree Cruickshank DPI: 0.326
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1840 4.88 %RANDOM
Rwork0.208 ---
obs0.21 37723 99.4 %-
Displacement parametersBiso max: 160.66 Å2 / Biso mean: 46.39 Å2 / Biso min: 14.39 Å2
Baniso -1Baniso -2Baniso -3
1--5.8826 Å20 Å20 Å2
2---5.8826 Å20 Å2
3---11.7652 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: final / Resolution: 2.66→116.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8620 0 163 76 8859
Biso mean--63.5 27.71 -
Num. residues----1028
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3246SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes254HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1324HARMONIC5
X-RAY DIFFRACTIONt_it8978HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1052SEMIHARMONIC5
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_contact9905SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d8978HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg12152HARMONIC20.95
X-RAY DIFFRACTIONt_omega_torsion2.57
X-RAY DIFFRACTIONt_other_torsion18.38
LS refinement shellResolution: 2.66→2.73 Å / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.283 146 5.08 %
Rwork0.237 2729 -
all-2875 -
obs--98.94 %
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)
10.8735-0.4615-0.07981.38010.65093.2536-0.0679-0.08860.02530.1749-0.02770.00780.0779-0.12380.0956-0.04570.02020.0202-0.07110.0026-0.1601-56.15799.832426.5219
20.98170.36720.05751.55810.66631.8445-0.05470.0887-0.02550.1956-0.01480.12810.2716-0.16340.0695-0.0308-0.0070.0089-0.0347-0.0099-0.1482-56.651-10.494-6.2445
32.58840.43470.53911.5608-0.32962.0675-0.05470.53130.0539-0.02340.0348-0.0371-0.13670.18360.0199-0.18040.04250.06450.02430.0023-0.1721-27.0935.7485-9.2501
42.2959-0.167-0.93990.84310.12662.3278-0.1786-0.5369-0.22140.0739-0.0887-0.13860.21030.2870.2673-0.10920.1050.00350.01170.0629-0.1883-25.298-4.180127.9344
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 256
2X-RAY DIFFRACTION2{ B|* }B1 - 258
3X-RAY DIFFRACTION3{ C|* }C1 - 256
4X-RAY DIFFRACTION4{ D|* }D1 - 258

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