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- PDB-2o8r: Crystal Structure of Polyphosphate Kinase from Porphyromonas Ging... -

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Basic information

Entry
Database: PDB / ID: 2o8r
TitleCrystal Structure of Polyphosphate Kinase from Porphyromonas Gingivalis
ComponentsPolyphosphate kinase
KeywordsTRANSFERASE / KINASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / PSI / NYSGRC / NEW YORK STRUCTURAL GENOMICS RESEARCH CONSORTIUM / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


polyphosphate kinase complex / ATP-polyphosphate phosphotransferase / polyphosphate biosynthetic process / polyphosphate kinase activity / ATP binding / metal ion binding
Similarity search - Function
Polyphosphate kinase N-terminal domain / polyphosphate kinase like / Polyphosphate kinase middle domain / Polyphosphate kinase / Polyphosphate kinase middle domain / Polyphosphate kinase N-terminal domain / Polyphosphate kinase C-terminal domain 2 / Polyphosphate kinase middle domain superfamily / Polyphosphate kinase N-terminal domain superfamily / Polyphosphate kinase, C-terminal domain 1 ...Polyphosphate kinase N-terminal domain / polyphosphate kinase like / Polyphosphate kinase middle domain / Polyphosphate kinase / Polyphosphate kinase middle domain / Polyphosphate kinase N-terminal domain / Polyphosphate kinase C-terminal domain 2 / Polyphosphate kinase middle domain superfamily / Polyphosphate kinase N-terminal domain superfamily / Polyphosphate kinase, C-terminal domain 1 / Polyphosphate kinase middle domain / Polyphosphate kinase N-terminal domain / Polyphosphate kinase C-terminal domain 2 / Polyphosphate kinase C-terminal domain 1 / Endonuclease Chain A / Endonuclease; Chain A / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Polyphosphate kinase
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsPatskovsky, Y. / Toro, R. / Sauder, J.M. / Dickey, M. / Adams, J.M. / Ozyurt, S. / Wasserman, S.R. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal Structure of Polyphosphate Kinase from Porphyromonas Gingivalis
Authors: Patskovsky, Y. / Toro, R. / Sauder, J.M. / Dickey, M. / Adams, J.M. / Ozyurt, S. / Wasserman, S.R. / Burley, S.K. / Almo, S.C.
History
DepositionDec 12, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Dec 27, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polyphosphate kinase
B: Polyphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,18315
Polymers165,9342
Non-polymers1,24913
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7300 Å2
ΔGint-212 kcal/mol
Surface area54980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.330, 99.330, 335.061
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B
14A
24B
15A
25B

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PHEPHEARGARGAA18 - 16520 - 167
21PHEPHEARGARGBB18 - 16520 - 167
12TYRTYRASNASNAA175 - 300177 - 302
22TYRTYRASNASNBB175 - 300177 - 302
13PROPROGLUGLUAA320 - 403322 - 405
23PROPROGLUGLUBB320 - 403322 - 405
14LEULEUILEILEAA414 - 640416 - 642
24LEULEUILEILEBB414 - 640416 - 642
15ARGARGTHRTHRAA675 - 690677 - 692
25ARGARGTHRTHRBB675 - 690677 - 692

NCS ensembles :
ID
1
2
3
4
5
Detailslikely homo-dimer, the asymmetric unit contains a homodimer

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Components

#1: Protein Polyphosphate kinase /


Mass: 82967.008 Da / Num. of mol.: 2 / Mutation: M1L, A635T, A690T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Strain: ATCC BAA-308 / W83 / Gene: ppk / Plasmid: BC-pSGX3(BC) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q7MTR1, ATP-polyphosphate phosphotransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.91 Å3/Da / Density % sol: 57.8 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.6M MALIC ACID, PH 7.0, 0.5M AMMONIUM SULFATE, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 / Wavelength: 0.9793 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 20, 2006 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 51199 / Num. obs: 51199 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 62.3 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.09 / Net I/σ(I): 6
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 1.8 / Rsym value: 0.48 / % possible all: 94.1

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Processing

Software
NameVersionClassification
SHELXmodel building
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.918 / SU B: 12.199 / SU ML: 0.249 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.612 / ESU R Free: 0.321 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25457 1578 3.1 %RANDOM
Rwork0.1879 ---
all0.19004 49169 --
obs0.19004 49169 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 0.8 Å / Solvent model: MASK
Displacement parametersBiso mean: 72.398 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å20.41 Å20 Å2
2--0.82 Å20 Å2
3----1.23 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10331 0 65 56 10452
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02210607
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3011.98114370
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.14451257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.00322.385520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.929151894
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.63915119
X-RAY DIFFRACTIONr_chiral_restr0.0880.21592
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027985
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1870.35091
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3220.57129
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.5662
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.369
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1890.513
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it8.30536440
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it10.771410243
X-RAY DIFFRACTIONr_scbond_it13.35344645
X-RAY DIFFRACTIONr_scangle_it16.84164120
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
11118medium positional0.460.5
2730medium positional0.410.5
3660medium positional0.380.5
41768medium positional0.540.5
5133medium positional0.320.5
11118medium thermal11.7110
2730medium thermal6.1310
3660medium thermal5.710
41768medium thermal10.4510
5133medium thermal6.2310
LS refinement shellResolution: 2.7→2.767 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 111 -
Rwork0.294 3537 -
obs-3537 98.33 %

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