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- PDB-6ioy: Crystal structure of Porphyromonas gingivalis acetate kinase -

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Basic information

Entry
Database: PDB / ID: 6ioy
TitleCrystal structure of Porphyromonas gingivalis acetate kinase
ComponentsAcetate kinase
KeywordsTRANSFERASE / Porphyromonas gingivalis / acetate kinase / ATP / essential gene
Function / homology
Function and homology information


acetate kinase / organic acid metabolic process / acetate kinase activity / acetyl-CoA biosynthetic process / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
Acetate and butyrate kinases family signature 2. / Acetate/propionate kinase / Aliphatic acid kinase, short-chain, conserved site / Acetate and butyrate kinases family signature 1. / Aliphatic acid kinase, short-chain / Acetokinase family / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsKezuka, Y. / Yoshida, Y. / Nonaka, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of ScienceJP16K11485 Japan
Japan Society for the Promotion of ScienceJP17K11634 Japan
CitationJournal: J Oral Microbiol / Year: 2019
Title: Characterization of the phosphotransacetylase-acetate kinase pathway for ATP production inPorphyromonas gingivalis.
Authors: Yoshida, Y. / Sato, M. / Nonaka, T. / Hasegawa, Y. / Kezuka, Y.
History
DepositionOct 31, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetate kinase
B: Acetate kinase
C: Acetate kinase
D: Acetate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,77911
Polymers175,0624
Non-polymers7177
Water17,547974
1
A: Acetate kinase
B: Acetate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,7454
Polymers87,5312
Non-polymers2142
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6570 Å2
ΔGint-84 kcal/mol
Surface area31630 Å2
MethodPISA
2
C: Acetate kinase
D: Acetate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,0347
Polymers87,5312
Non-polymers5025
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7220 Å2
ΔGint-131 kcal/mol
Surface area30020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.770, 98.472, 102.769
Angle α, β, γ (deg.)90.00, 91.64, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUAA0 - 3975 - 402
21LEULEUBB0 - 3975 - 402
12ILEILEAA0 - 3965 - 401
22ILEILECC0 - 3965 - 401
13ILEILEAA0 - 3965 - 401
23ILEILEDD0 - 3965 - 401
14ILEILEBB0 - 3965 - 401
24ILEILECC0 - 3965 - 401
15ILEILEBB0 - 3965 - 401
25ILEILEDD0 - 3965 - 401
16LEULEUCC0 - 3975 - 402
26LEULEUDD0 - 3975 - 402

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Acetate kinase / Acetokinase


Mass: 43765.555 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561) (bacteria)
Strain: ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561
Gene: ackA, PGN_1178 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B2RK02, acetate kinase
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 974 / 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: 2.39 Å3/Da / Density % sol: 48.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M lithium sulfate monohydrate, 0.1 M Tris/HCl (pH 8.5), and 24% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.94→53.4 Å / Num. obs: 120952 / % possible obs: 99.3 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 11.9
Reflection shellResolution: 1.94→1.97 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 5.78 / Num. unique obs: 5602 / % possible all: 92.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
DIALSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IIR

2iir


Resolution: 1.94→53.4 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.917 / SU B: 3.435 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.147 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21942 6081 5 %RANDOM
Rwork0.18919 ---
obs0.1907 114747 99.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 18.041 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å20 Å2-0.62 Å2
2---0.53 Å20 Å2
3---1.1 Å2
Refinement stepCycle: 1 / Resolution: 1.94→53.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12114 0 41 974 13129
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01412386
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711725
X-RAY DIFFRACTIONr_angle_refined_deg1.371.60216716
X-RAY DIFFRACTIONr_angle_other_deg0.9481.63827424
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.42451602
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.76223.051531
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.833152253
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4521557
X-RAY DIFFRACTIONr_chiral_restr0.0740.21630
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.01913767
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0192129
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6191.626402
X-RAY DIFFRACTIONr_mcbond_other1.6181.626401
X-RAY DIFFRACTIONr_mcangle_it2.5252.4228000
X-RAY DIFFRACTIONr_mcangle_other2.5252.4228001
X-RAY DIFFRACTIONr_scbond_it2.5161.9675984
X-RAY DIFFRACTIONr_scbond_other2.5151.9675985
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9642.8128715
X-RAY DIFFRACTIONr_long_range_B_refined5.33219.75413786
X-RAY DIFFRACTIONr_long_range_B_other5.22519.50413530
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A124660.08
12B124660.08
21A124780.08
22C124780.08
31A121970.09
32D121970.09
41B123900.08
42C123900.08
51B120640.1
52D120640.1
61C122480.09
62D122480.09
LS refinement shellResolution: 1.94→1.99 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 450 -
Rwork0.229 7888 -
obs--93.52 %

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