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- PDB-3rhf: Crystal structure of Polyphosphate Kinase 2 from Arthrobacter aur... -

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Basic information

Entry
Database: PDB / ID: 3rhf
TitleCrystal structure of Polyphosphate Kinase 2 from Arthrobacter aurescens TC1
ComponentsPutative polyphosphate kinase 2 family protein
KeywordsTRANSFERASE / PSI-biology / MCSG / Structural Genomics / Midwest Center for Structural Genomics / 3-layer alpha/beta/alpha sandwich with the central 5-stranded
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
CITRATE ANION / TRIETHYLENE GLYCOL / PHOSPHATE ION / Putative polyphosphate kinase 2 family protein
Similarity search - Component
Biological speciesArthrobacter aurescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.45 Å
AuthorsNocek, B. / Hatzos-Skintges, C. / Feldmann, B. / Babnigg, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of Polyphosphate Kinase 2 from Arthrobacter aurescens TC1
Authors: Nocek, B. / Hatzos-Skintges, C. / Feldmann, B. / Babnigg, G. / Joachimiak, A.
History
DepositionApr 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative polyphosphate kinase 2 family protein
B: Putative polyphosphate kinase 2 family protein
C: Putative polyphosphate kinase 2 family protein
D: Putative polyphosphate kinase 2 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,25227
Polymers129,1984
Non-polymers3,05323
Water8,305461
1
A: Putative polyphosphate kinase 2 family protein
C: Putative polyphosphate kinase 2 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,00913
Polymers64,5992
Non-polymers1,41011
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6720 Å2
ΔGint-32 kcal/mol
Surface area24130 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16640 Å2
ΔGint-54 kcal/mol
Surface area45700 Å2
MethodPISA
3
B: Putative polyphosphate kinase 2 family protein
D: Putative polyphosphate kinase 2 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,24314
Polymers64,5992
Non-polymers1,64412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7220 Å2
ΔGint-16 kcal/mol
Surface area24270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.353, 126.353, 199.064
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Putative polyphosphate kinase 2 family protein


Mass: 32299.553 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter aurescens (bacteria) / Strain: TC1 / Gene: AAur_2811 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: A1R8G0

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Non-polymers , 7 types, 484 molecules

#2: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical
ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H5O7
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#5: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 461 / 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: 3.07 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.1 M Phosphate Citrate, 40% PEG 300, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 5, 2011 / Details: mirror
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.45→40 Å / Num. all: 59938 / Num. obs: 59938 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Biso Wilson estimate: 47.6 Å2 / Rmerge(I) obs: 0.153 / Net I/σ(I): 15
Reflection shellResolution: 2.45→2.49 Å / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
PHENIXmodel building
SHELXmodel building
ARP/wARPmodel building
MLPHAREphasing
REFMAC5.5.0109refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.45→40 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.914 / SU B: 15.068 / SU ML: 0.158 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.325 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.235 3005 5 %RANDOM
Rwork0.18429 ---
all0.19 59634 --
obs0.18685 56629 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.39 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20 Å20 Å2
2--0.64 Å20 Å2
3----1.28 Å2
Refinement stepCycle: LAST / Resolution: 2.45→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8770 0 193 461 9424
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0229130
X-RAY DIFFRACTIONr_bond_other_d0.0010.026236
X-RAY DIFFRACTIONr_angle_refined_deg1.7781.96912335
X-RAY DIFFRACTIONr_angle_other_deg1.11315157
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.24651119
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.8424.13414
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.768151512
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0551560
X-RAY DIFFRACTIONr_chiral_restr0.1310.21328
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02110103
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021829
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_it0.8091.55588
X-RAY DIFFRACTIONr_mcbond_other0.1451.52287
X-RAY DIFFRACTIONr_mcangle_it1.58328905
X-RAY DIFFRACTIONr_scbond_it2.75533542
X-RAY DIFFRACTIONr_scangle_it4.4354.53430
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.449→2.512 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 180 -
Rwork0.272 4102 -
obs--98.41 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.9461-6.30071.110913.25650.34732.6649-0.0804-0.1097-0.18480.30290.13880.37060.0706-0.3453-0.05840.166-0.0245-0.03180.2973-0.02080.195651.586528.775882.3215
20.6955-1.61370.38142.1721-0.36881.66250.12450.0747-0.0842-0.216-0.07930.19910.0476-0.1582-0.04520.2105-0.0264-0.04290.2819-0.01960.183956.342128.567877.2
3-0.59810.71011.8446-0.3381-0.439410.6058-0.163-0.10470.30320.0488-0.09540.236-0.2631-0.21220.25840.26450.0631-0.03790.2615-0.03040.263660.272136.738996.5865
40.2886-1.7698-0.87684.8920.34973.16930.0454-0.0037-0.08440.1165-0.09340.1784-0.0181-0.00280.0480.23890.0452-0.02960.2971-0.00810.175564.577929.8197106.1376
50.5033-0.39550.03280.9575-0.49760.7383-0.0099-0.04920.0315-0.0948-0.04570.03960.10840.09130.05550.25720.0192-0.01370.2262-0.010.194175.702523.719388.4534
62.5789-1.5085-2.72452.6026-0.03692.5025-0.2138-0.16140.04520.10740.2048-0.04210.10590.06590.0090.22350.0179-0.04070.2376-0.01760.217973.093423.97595.844
71.271-0.95510.11980.39630.35462.80180.03150.0099-0.1683-0.0545-0.08410.08690.25060.35010.05260.34090.07670.02560.20160.01720.218973.85239.286885.7396
80.93530.3771-0.80390.6385-0.93513.9149-0.01540.0874-0.0997-0.13980.0150.0910.2405-0.06940.00040.27380.058-0.02190.2199-0.050.169867.540322.834178.2196
94.52713.02482.65647.51973.10181.56780.02590.0147-0.00260.00590.044-0.30240.08060.0545-0.070.30840.05620.06520.2518-0.03260.109980.419829.425967.7789
100.5293-0.3457-0.23460.7862-0.09810.66510.03870.07260.0029-0.1607-0.02140.04480.2254-0.1218-0.01730.2994-0.0013-0.03710.2173-0.03090.197763.918919.273278.8952
11-0.1180.2923-0.20122.99323.4476.04440.00220.00570.0130.1999-0.1280.11660.294-0.2530.12580.18190.0069-0.01350.2643-0.01290.236257.876234.7074105.6556
125.41382.6874-2.2603-1.45440.15125.31510.16930.05040.28090.16230.03660.1618-0.3023-0.1541-0.20590.2640.04010.03710.2338-0.00440.224963.43353.3041120.2842
1318.5612-7.3660.99663.3661-0.80951.1375-0.0330.1872-0.5678-0.08790.08650.09880.2623-0.0938-0.05350.26580.01830.01930.18750.03430.202891.3527-10.7049116.9072
141.2258-2.05030.87271.1807-1.21911.5624-0.0463-0.2092-0.41770.13910.25860.22840.1319-0.1448-0.21230.2601-0.01840.03750.24950.05530.238589.2756-6.9519125.69
151.056-0.38640.70560.5306-1.13282.5365-0.00750.07870.0094-0.0486-0.0554-0.02190.02640.16760.06290.25790.03440.01410.22560.00920.193599.3294-0.6792103.3208
160.2145-0.32020.09520.2887-0.12870.71480.0168-0.020.0530.0410.0117-0.0612-0.0947-0.041-0.02850.26220.01080.02370.22440.01260.221993.95487.7515113.2983
1710.0645-6.4981-0.93663.57750.71971.1178-0.0826-0.16560.3059-0.11860.0603-0.2948-0.2682-0.09420.02230.3260.03150.02070.2030.05510.203484.005719.6923110.3112
183.4681-1.03691.36365.3077-3.35470.4161-0.12110.0544-0.0074-0.01350.0570.1008-0.01910.02550.06410.24920.0511-0.01070.23250.00290.211676.274317.7805106.7174
191.2766-0.8631-0.21330.7167-0.06710.9099-0.0138-0.0271-0.07030.04240.05280.043-0.1054-0.129-0.0390.24260.02760.02290.22610.04120.208978.13918.5164110.9455
202.2463.92952.38997.13132.1683.63990.0101-0.1341-0.01630.1889-0.02620.01970.034-0.00740.01610.26160.03960.05460.29990.0240.139491.81859.3409133.7263
214.68432.2037-1.8584.4644-2.97361.2196-0.03710.1082-0.1068-0.0253-0.00450.0202-0.04910.00690.04160.25250.04470.07540.2775-0.06840.161192.130618.386131.2785
220.8156-0.4222-0.03110.6904-0.19910.628-0.0407-0.0395-0.00480.07580.09620.06140.0446-0.0597-0.05540.23620.01410.0180.23450.04450.213484.83360.4492119.9276
234.82541.1783-7.00150.1378-1.466210.4572-0.2460.24-0.2111-0.08090.0837-0.03450.3608-0.35260.16240.26710.0050.01970.20150.01190.2237100.0031-3.870290.8969
242.7438-1.44620.79694.68992.56763.6119-0.26380.019-0.1019-0.45920.4185-0.2008-0.17920.118-0.15470.2563-0.02510.04180.2733-0.05830.194116.57673.238678.2434
254.6614-0.93522.94241.2844-0.81995.86390.04680.42710.1589-0.3591-0.1002-0.2369-0.38480.37550.05340.3070.03850.04070.18820.04960.188180.779662.499787.7606
261.2827-0.72-0.20331.0880.22971.35160.15030.13370.0995-0.2373-0.12580.022-0.2455-0.2065-0.02450.21730.04220.01610.20060.03410.174376.95255.950589.2043
271.1014-0.336-0.65860.18540.37861.46860.0130.0607-0.0064-0.0534-0.03330.01910.0012-0.02710.02030.25720.00480.00480.2009-0.00420.226782.591244.534992.0487
280.8636-0.4450.92570.4874-0.37661.49950.0334-0.0109-0.07790.01060.04710.03170.1095-0.0402-0.08050.24610.00650.00680.2153-0.00680.223386.69936.2758101.2208
290.46950.3507-0.02260.32070.52661.7774-0.0110.03840.07030.1062-0.01920.04830.18330.05530.03020.25550.0058-0.00560.2137-0.01390.224486.799743.5212100.2241
304.25871.38960.81674.54130.84113.16820.26-0.21980.20830.6407-0.07940.03060.1822-0.1865-0.18060.3414-0.03480.00090.1985-0.06420.213594.905548.3238115.7189
310.631-0.3817-0.02780.7035-0.54320.95390.07870.04640.0537-0.0306-0.011-0.0963-0.08910.1041-0.06770.2282-0.0112-0.0010.2194-0.02610.231995.033447.214897.5403
321.89480.8212-0.28020.62-0.45111.13190.077-0.06280.17010.0366-0.02780.1677-0.1105-0.1426-0.04910.25280.03220.01830.22320.00050.211466.736553.7697108.9467
331.24550.9697-0.6040.6482-0.73020.60210.027-0.0284-0.1126-0.06080.0067-0.09370.03690.0012-0.03370.26520.0099-0.00980.2096-0.02730.235270.592748.3995114.0758
346.2826-1.2347-6.10332.079-0.03065.91490.3533-0.20360.28820.1027-0.1371-0.1199-0.4010.1836-0.21620.241-0.0165-0.01150.2231-0.04210.223787.9756.8386109.327
350.25970.00170.10550.35770.54491.31920.09950.12990.0798-0.0932-0.0227-0.0689-0.1016-0.059-0.07680.25810.01620.02130.21510.02930.220982.678852.388787.9937
36-4.12963.1289-3.63119.10530.04994.7192-0.16320.2582-0.1359-0.32850.5014-0.03520.33930.6999-0.33820.35460.04170.0420.4365-0.18340.108181.946127.218358.6096
372.6641-1.50041.71834.7799-3.34966.1498-0.1027-0.03660.10790.50580.1693-0.6276-0.16360.6343-0.06660.16330.0345-0.0940.3202-0.08450.205125.703521.3869109.9262
381.4906-0.7156-0.43711.45630.16851.5981-0.0899-0.2504-0.02670.18610.1185-0.15780.18260.314-0.02860.17110.0246-0.0550.2342-0.02640.1799119.267316.2872109.6846
390.6447-0.4943-0.7981.24690.63632.1831-0.0689-0.0736-0.0390.13780.06610.01250.06890.11310.00290.2092-0.0038-0.00320.2567-0.00370.1918106.229120.1962108.2901
401.6866-0.70330.82521.9183-1.3541.27680.0051-0.0254-0.0122-0.0651-0.0690.1134-0.0411-0.15770.06380.23880.0387-0.01970.2383-0.03520.213198.097727.448793.3706
410.0902-0.4295-0.25041.4735-0.69742.12150.02940.037-0.0747-0.0455-0.0633-0.03760.028-0.11620.03390.2082-0.0131-0.0110.2244-0.02560.2334104.908425.804999.1505
421.0028-2.88641.5132-1.04821.99682.69650.31260.24680.1698-0.1551-0.2612-0.2412-0.3057-0.1341-0.05140.37950.01710.12770.2410.0120.2672109.132234.46183.3072
430.36450.22150.02021.7450.29522.0618-0.0142-0.03320.00520.0220.00250.0572-0.29910.00960.01180.2319-0.00750.00450.2063-0.02120.2164109.102234.0801101.5739
440.26560.8760.30543.21981.12161.2710.00660.0635-0.0936-0.01640.024-0.1570.13420.1531-0.03060.19590.0270.00060.265-0.01470.2223117.76576.752989.5284
451.07242.3588-0.34945.0611-0.94930.29710.1077-0.0463-0.00540.1187-0.00430.026-0.02010.0608-0.10350.22420.01260.03410.2654-0.00790.212112.647611.849385.0935
460.565-0.91350.2151.6521-0.07261.4371-0.0078-0.06410.02660.01160.1073-0.1749-0.05390.231-0.09950.1771-0.01710.00320.2497-0.03170.2314119.281522.8238100.3009
475.9436-1.3227-7.18413.38562.81859.14290.1619-0.17370.07150.2949-0.0046-0.151-0.14190.2351-0.15730.26650.018-0.04860.22520.02670.1358108.285925.5584122.714
4814.72688.51120.468511.0826-5.17334.67470.718-0.93150.65690.7019-0.52960.7365-0.213-0.1132-0.18840.3726-0.01180.13520.3489-0.06040.040790.884718.6809141.5623
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 18
2X-RAY DIFFRACTION2A19 - 52
3X-RAY DIFFRACTION3A53 - 60
4X-RAY DIFFRACTION4A61 - 72
5X-RAY DIFFRACTION5A73 - 122
6X-RAY DIFFRACTION6A123 - 136
7X-RAY DIFFRACTION7A137 - 171
8X-RAY DIFFRACTION8A172 - 196
9X-RAY DIFFRACTION9A197 - 215
10X-RAY DIFFRACTION10A216 - 257
11X-RAY DIFFRACTION11A258 - 277
12X-RAY DIFFRACTION12A278 - 286
13X-RAY DIFFRACTION13B6 - 19
14X-RAY DIFFRACTION14B20 - 41
15X-RAY DIFFRACTION15B42 - 72
16X-RAY DIFFRACTION16B73 - 101
17X-RAY DIFFRACTION17B102 - 113
18X-RAY DIFFRACTION18B114 - 123
19X-RAY DIFFRACTION19B124 - 183
20X-RAY DIFFRACTION20B184 - 199
21X-RAY DIFFRACTION21B200 - 216
22X-RAY DIFFRACTION22B217 - 260
23X-RAY DIFFRACTION23B261 - 277
24X-RAY DIFFRACTION24B278 - 286
25X-RAY DIFFRACTION25C6 - 18
26X-RAY DIFFRACTION26C19 - 63
27X-RAY DIFFRACTION27C64 - 92
28X-RAY DIFFRACTION28C93 - 125
29X-RAY DIFFRACTION29C126 - 145
30X-RAY DIFFRACTION30C146 - 159
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