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- PDB-5ld1: Crystal Structure of Polyphosphate Kinase from Meiothermus ruber ... -

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Basic information

Entry
Database: PDB / ID: 5ld1
TitleCrystal Structure of Polyphosphate Kinase from Meiothermus ruber bound to ATP
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-5'-TRIPHOSPHATE / Polyphosphate:AMP phosphotransferase
Similarity search - Component
Biological speciesMeiothermus ruber (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.09 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 23, 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 2.0Jan 10, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_conn_angle / software / struct_conn
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _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)139,90925
Polymers135,1134
Non-polymers4,79621
Water15,745874
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20540 Å2
ΔGint-177 kcal/mol
Surface area42300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.014, 168.014, 95.032
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11C-1287-

HOH

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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 (bacteria) / Gene: MrH_2468 / Plasmid: pET28A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0S7ASE9

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Non-polymers , 5 types, 895 molecules

#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 874 / 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: 2.48 Å3/Da / Density % sol: 50.44 %
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: X06SA / 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: 2.09→168.01 Å / Num. obs: 80333 / % possible obs: 100 % / Redundancy: 18.4 % / Biso Wilson estimate: 29.36 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.26 / Rsym value: 0.264 / Net I/σ(I): 11.7
Reflection shellResolution: 2.09→2.21 Å / Redundancy: 19.2 % / Rmerge(I) obs: 1.586 / Mean I/σ(I) obs: 2.4 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.595
Highest resolutionLowest resolution
Rotation118.81 Å2.2 Å
Translation118.81 Å2.2 Å

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Processing

Software
NameVersionClassification
Aimless0.5.15data scaling
MOLREP11.4.05phasing
BUSTER-TNT2.10.3refinement
PDB_EXTRACT3.2data extraction
autoPROC1.0.5data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LC9

5lc9


Resolution: 2.09→118.8 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.929 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.168 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.181 / SU Rfree Blow DPI: 0.152 / SU Rfree Cruickshank DPI: 0.148
RfactorNum. reflection% reflectionSelection details
Rfree0.202 3972 4.95 %RANDOM
Rwork0.163 ---
obs0.165 80254 99.5 %-
Displacement parametersBiso max: 141.57 Å2 / Biso mean: 32.44 Å2 / Biso min: 10.03 Å2
Baniso -1Baniso -2Baniso -3
1--1.0653 Å20 Å20 Å2
2---1.0653 Å20 Å2
3---2.1305 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: final / Resolution: 2.09→118.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8705 0 287 874 9866
Biso mean--27.49 35.48 -
Num. residues----1039
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3370SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes258HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1404HARMONIC5
X-RAY DIFFRACTIONt_it9235HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1090SEMIHARMONIC5
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_contact11213SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d9235HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg12538HARMONIC20.97
X-RAY DIFFRACTIONt_omega_torsion3.42
X-RAY DIFFRACTIONt_other_torsion17
LS refinement shellResolution: 2.09→2.14 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.223 277 5.04 %
Rwork0.192 5223 -
all-5500 -
obs--93.2 %
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)
10.54840.1768-0.24150.7009-0.08431.0489-0.0249-0.0757-0.05590.0629-0.00750.04750.2016-0.11160.0324-0.048-0.02860.0383-0.04180.0188-0.1055-9.9051-58.38150.0409
20.6864-0.1395-0.20710.6488-0.00371.0476-0.03780.0332-0.0826-0.0734-0.0304-0.03470.24660.0820.0682-0.01070.01640.0384-0.058-0.0074-0.10311.0447-58.7483-32.6052
31.0737-0.2329-0.17511.01330.35810.91450.06130.2670.133-0.2585-0.09670.0514-0.2532-0.16910.0354-0.05720.0516-0.0171-0.07150.0528-0.126-2.4716-28.1274-35.8474
40.8907-0.06880.14710.9166-0.26381.1233-0.0436-0.17680.1790.1861-0.0254-0.0585-0.26240.0310.0689-0.04080.0062-0.0202-0.0777-0.0384-0.06752.8159-27.26381.8364
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 257
2X-RAY DIFFRACTION2{ B|* }B1 - 267
3X-RAY DIFFRACTION3{ C|* }C1 - 267
4X-RAY DIFFRACTION4{ D|* }D1 - 267

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