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- PDB-5ldb: Crystal Structure of Polyphosphate Kinase from Meiothermus ruber ... -

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Basic information

Entry
Database: PDB / ID: 5ldb
TitleCrystal Structure of Polyphosphate Kinase from Meiothermus ruber bound to ADP
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
ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / Polyphosphate:AMP phosphotransferase
Similarity search - Component
Biological speciesMeiothermus ruber H328 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 24, 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_conn_angle / software / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _software.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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)137,42718
Polymers135,1134
Non-polymers2,31314
Water8,755486
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16100 Å2
ΔGint-131 kcal/mol
Surface area43350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.619, 165.619, 95.150
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
Source: (gene. exp.) Meiothermus ruber H328 (bacteria) / Gene: MrH_2468 / Plasmid: pET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0S7ASE9

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Non-polymers , 6 types, 500 molecules

#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


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


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 486 / 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: 2.41 Å3/Da / Density % sol: 49.06 % / Mosaicity: 0.08 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: PEG3350, Li2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00001 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 14, 2015 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 2.3→47.75 Å / Num. obs: 59190 / % possible obs: 100 % / Redundancy: 27 % / Biso Wilson estimate: 38.46 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.47 / Rsym value: 0.488 / Net I/σ(I): 10.3
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 28.2 % / Rmerge(I) obs: 4.798 / Mean I/σ(I) obs: 1.1 / Rsym value: 4.97 / % possible all: 100

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Processing

Software
NameVersionClassification
autoPROCdata collection
Aimless0.5.25data scaling
BUSTER-TNT2.10.3refinement
PDB_EXTRACT3.2data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LC9

5lc9


Resolution: 2.3→47.75 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.923 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.268 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.279 / SU Rfree Blow DPI: 0.192 / SU Rfree Cruickshank DPI: 0.192
RfactorNum. reflection% reflectionSelection details
Rfree0.21 2935 4.96 %RANDOM
Rwork0.177 ---
obs0.179 59125 100 %-
Displacement parametersBiso max: 205.86 Å2 / Biso mean: 48.35 Å2 / Biso min: 11.11 Å2
Baniso -1Baniso -2Baniso -3
1--2.5785 Å20 Å20 Å2
2---2.5785 Å20 Å2
3---5.1571 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: final / Resolution: 2.3→47.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8707 0 187 486 9380
Biso mean--49.31 40.23 -
Num. residues----1039
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3316SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes260HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1356HARMONIC5
X-RAY DIFFRACTIONt_it9127HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1073SEMIHARMONIC5
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_contact10391SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d9127HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg12395HARMONIC21
X-RAY DIFFRACTIONt_omega_torsion3.21
X-RAY DIFFRACTIONt_other_torsion18.08
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 228 5.3 %
Rwork0.238 4076 -
all-4304 -
obs--100 %
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)
11.5063-0.0952-0.89730.67420.15321.9138-0.0466-0.2073-0.08-0.1077-0.0343-0.01920.22190.33110.0810.03170.02560.0137-0.01040.016-0.1527176.364108.52917.6267
21.10480.3248-0.62710.8943-0.29123.0353-0.024-0.17620.00930.0836-0.04170.08960.16340.09580.0657-0.019-0.03390.01690.01310.0061-0.1484155.791109.06750.2977
31.27980.25480.28642.4201-1.06462.8150.0544-0.24840.23190.5651-0.3452-0.0943-0.48580.34670.2908-0.0188-0.0918-0.0172-0.0262-0.0309-0.1989169.514139.38651.7493
41.0080.07990.04012.49220.71331.4868-0.0450.08640.1013-0.8507-0.07030.2441-0.426-0.1850.11530.17840.0562-0.0837-0.15520.0408-0.1596160.384137.8614.5025
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 258
2X-RAY DIFFRACTION2{ B|* }B1 - 267
3X-RAY DIFFRACTION3{ C|* }C1 - 267
4X-RAY DIFFRACTION4{ D|* }D1 - 267

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