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- PDB-7w1f: Crystal structure of the dNTP triphosphohydrolase PA1124 from Pse... -

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Basic information

Entry
Database: PDB / ID: 7w1f
TitleCrystal structure of the dNTP triphosphohydrolase PA1124 from Pseudomonas aeruginosa
ComponentsProbable deoxyguanosinetriphosphate triphosphohydrolase
KeywordsHYDROLASE / dNTP triphosphohydrolase / PA1124 / Pseudomonas aeruginosa
Function / homology
Function and homology information


dGTPase / dGTPase activity / dGTP catabolic process / magnesium ion binding
Similarity search - Function
dNTP triphosphohydrolase, type 1 / Deoxyguanosinetriphosphate triphosphohydrolase, central domain superfamily / dNTP triphosphohydrolase / HD domain profile. / HD domain / HD domain / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain
Similarity search - Domain/homology
NICKEL (II) ION / Probable deoxyguanosinetriphosphate triphosphohydrolase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsOh, H.B. / Song, W.S. / Lee, K.C. / Park, S.C. / Yoon, S.I.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2022
Title: Structural analysis of the dNTP triphosphohydrolase PA1124 from Pseudomonas aeruginosa.
Authors: Oh, H.B. / Lee, K.C. / Park, S.C. / Song, W.S. / Yoon, S.I.
History
DepositionNov 19, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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: Probable deoxyguanosinetriphosphate triphosphohydrolase
B: Probable deoxyguanosinetriphosphate triphosphohydrolase
C: Probable deoxyguanosinetriphosphate triphosphohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,0716
Polymers171,8953
Non-polymers1763
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-63 kcal/mol
Surface area55550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.077, 131.017, 136.462
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEPROPRO(chain 'A' and ((resid 11 through 14 and (name N...AA11 - 1617 - 22
12ASPASPLYSLYS(chain 'A' and ((resid 11 through 14 and (name N...AA29 - 19935 - 205
13GLYGLYVALVAL(chain 'A' and ((resid 11 through 14 and (name N...AA223 - 238229 - 244
14ARGARGALAALA(chain 'A' and ((resid 11 through 14 and (name N...AA242 - 318248 - 324
15GLUGLULEULEU(chain 'A' and ((resid 11 through 14 and (name N...AA321 - 333327 - 339
16VALVALGLNGLN(chain 'A' and ((resid 11 through 14 and (name N...AA335 - 430341 - 436
17PROPROVALVAL(chain 'A' and ((resid 11 through 14 and (name N...AA434 - 458440 - 464
18GLUGLULEULEU(chain 'A' and ((resid 11 through 14 and (name N...AA460 - 463466 - 469
19ARGARGLEULEU(chain 'A' and ((resid 11 through 14 and (name N...AA465 - 498471 - 504
21ILEILEPROPRO(chain 'B' and ((resid 11 through 14 and (name N...BB11 - 1617 - 22
22ASPASPLYSLYS(chain 'B' and ((resid 11 through 14 and (name N...BB29 - 19935 - 205
23GLYGLYVALVAL(chain 'B' and ((resid 11 through 14 and (name N...BB223 - 238229 - 244
24ARGARGALAALA(chain 'B' and ((resid 11 through 14 and (name N...BB242 - 318248 - 324
25GLUGLULEULEU(chain 'B' and ((resid 11 through 14 and (name N...BB321 - 333327 - 339
26VALVALGLNGLN(chain 'B' and ((resid 11 through 14 and (name N...BB335 - 430341 - 436
27PROPROVALVAL(chain 'B' and ((resid 11 through 14 and (name N...BB434 - 458440 - 464
28GLUGLULEULEU(chain 'B' and ((resid 11 through 14 and (name N...BB460 - 463466 - 469
29ARGARGLEULEU(chain 'B' and ((resid 11 through 14 and (name N...BB465 - 498471 - 504
31ILEILEPROPRO(chain 'C' and (resid 11 through 17 or (resid 29...CC11 - 1617 - 22
32ASPASPLYSLYS(chain 'C' and (resid 11 through 17 or (resid 29...CC29 - 19935 - 205
33GLYGLYVALVAL(chain 'C' and (resid 11 through 17 or (resid 29...CC223 - 238229 - 244
34ARGARGALAALA(chain 'C' and (resid 11 through 17 or (resid 29...CC242 - 318248 - 324
35GLUGLULEULEU(chain 'C' and (resid 11 through 17 or (resid 29...CC321 - 333327 - 339
36VALVALGLNGLN(chain 'C' and (resid 11 through 17 or (resid 29...CC335 - 430341 - 436
37PROPROVALVAL(chain 'C' and (resid 11 through 17 or (resid 29...CC434 - 458440 - 464
38GLUGLULEULEU(chain 'C' and (resid 11 through 17 or (resid 29...CC460 - 463466 - 469
39ARGARGLEULEU(chain 'C' and (resid 11 through 17 or (resid 29...CC465 - 498471 - 504

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Components

#1: Protein Probable deoxyguanosinetriphosphate triphosphohydrolase / dGTP triphosphohydrolase / dGTPase


Mass: 57298.199 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: dgt, CGU42_27675, DT376_15175, ECC04_023415, GNQ48_17405, IPC1339_07895
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0Q3JKU0, dGTPase
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 2.29 Å3/Da / Density % sol: 46.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: PEG 2000, calcium acetate, Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 34710 / % possible obs: 97.4 % / Redundancy: 3.8 % / Biso Wilson estimate: 89.31 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 29.2
Reflection shellResolution: 2.9→3 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3459 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X9E

4x9e


Resolution: 2.9→29.66 Å / SU ML: 0.4308 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.7596
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2735 1660 4.79 %
Rwork0.2304 32995 -
obs0.2325 34655 97.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 104.9 Å2
Refinement stepCycle: LAST / Resolution: 2.9→29.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10318 0 0 0 10318
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005210533
X-RAY DIFFRACTIONf_angle_d0.745214358
X-RAY DIFFRACTIONf_chiral_restr0.04381632
X-RAY DIFFRACTIONf_plane_restr0.00641920
X-RAY DIFFRACTIONf_dihedral_angle_d25.75613656
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.990.40881170.31752740X-RAY DIFFRACTION98.31
2.99-3.080.32871280.3072763X-RAY DIFFRACTION99.38
3.08-3.190.34331400.28962759X-RAY DIFFRACTION98.71
3.19-3.320.34161520.28372758X-RAY DIFFRACTION98.81
3.32-3.470.32531420.25792742X-RAY DIFFRACTION98.7
3.47-3.650.33241450.24412751X-RAY DIFFRACTION97.97
3.65-3.880.2721410.2352742X-RAY DIFFRACTION98.23
3.88-4.180.28491530.22342736X-RAY DIFFRACTION97.5
4.18-4.60.25021170.20212768X-RAY DIFFRACTION97.14
4.6-5.260.28781420.21282769X-RAY DIFFRACTION97.07
5.26-6.620.29961640.25712713X-RAY DIFFRACTION95.45
6.62-29.660.18351190.19852754X-RAY DIFFRACTION90.77
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)
12.78973521731-0.5088264930160.8340864725423.375901177661.064894102291.6502891509-0.463995540168-0.400264449112-0.3165097056041.261732809370.3812521459350.1911256294490.319629054188-0.0826055084970.04700591111951.682400787510.1012076643920.1676097997920.4630355232880.06882112346030.811715754305-6.69773518191-0.02053515322713.2231632486
21.27009087091-0.1678928588790.2262210298271.505622463041.029034653173.15357071577-0.349413331777-0.177847331840.2510154869520.824090245157-0.02082250940420.2397274398840.00364949469024-0.4738745388470.3541060333361.278480342170.06128057549830.1422099317670.45442688223-0.06747979867230.928678565077-15.30582105868.047764059535.94448741384
31.6896444133-1.69620229966-0.04319919920373.49494354256-0.9762418741123.90687244829-0.423195686480.0489085828086-0.9009219907860.449846896371-0.1485274477030.487317972380.992375892022-1.021972068670.5110040017771.17829380742-0.3742225318360.4237535834510.675004100654-0.2467203373691.00703606936-21.1874620031-15.8135351859-9.27265082449
41.523573757250.0298713938948-0.1278136899732.92968587770.9027428325231.494174355760.1557075998090.7046009445710.646906707116-0.57555179369-0.4034910031570.266620107494-0.523674524702-0.1010216786340.2581951172160.800622781732-0.00317124281123-0.2164148402251.004466508080.2515662020340.786240740274-16.887057282128.2991979454-43.1353329306
56.11588038162-2.28107528998-1.701063703743.738606584550.1900489330161.270446656840.2288586855712.019267650680.77561643256-0.649223558381-0.4724361924190.251963495169-0.459796065181-0.5222413403370.2100803575851.08664749519-0.141414222192-0.2598721245421.190556377820.298494768810.788017575252-20.24085817327.9042418984-46.1133955191
62.34506038325-0.210463346347-0.5177287881582.48793927695-0.8687777229471.620966256720.04894391483551.80307681380.678841447835-1.04478791555-0.1641866764520.1593379560690.0743531010197-0.07140378579990.1311992266211.14906180543-0.100695362315-0.2000105432611.824862367440.2252288399160.830828483653-10.148722870518.1406218632-58.3814391867
75.88667851563-1.934008375731.333650721891.26375658425-1.242536597851.41905269402-0.3280541907720.2809845645710.6238465730460.5645517035740.0143181636954-0.0674014847003-0.308105491972-0.05976501800030.3118270775850.719398037267-0.162246252862-0.04610081889770.480179840757-0.02471421876890.594065283899-24.141290747720.1583871522-23.1140899398
81.08097962589-1.21593899461-0.9919459988743.26310004318-0.2737833301771.64389037470.1494953854290.919020757207-0.815141030952-0.336043217386-0.4601199546820.7080819957860.714257311946-0.5989676697470.3034178825551.11030070587-0.3103383845410.0748635430881.2693940504-0.6993475607031.27595864259-13.3336279698-29.6772473979-43.9121938777
90.04330022031490.400235425530.1946846293451.871883122580.5257390491490.657904196801-0.3141055476380.34641079056-0.416540945449-0.263671646565-0.3312752996790.863850102142-0.214919184979-0.4992145178030.665010071581.25107684702-0.3909061295680.2309502973831.27336792416-0.6503516432331.65521640169-15.0663857024-34.7869439983-38.1791738753
101.915583101522.015411046122.552767041153.05429630842.515866211863.194293837490.327631680149-0.184875304753-1.776245738120.597343332689-0.254996172947-0.6327846701731.52852137585-0.55300989957-0.0700252515791.59936084495-0.2370941967130.3022625917710.749774093631-0.1226649721731.448580032252.17619287299-45.5999283265-23.6535358863
111.84428387842-0.482838595023-0.0887088313721.474329556030.4579011697671.07968858101-0.0685154021850.1712571585-0.992725203531-0.0378912877796-0.2080487042480.8356951859080.757939018303-0.5151218675470.269182200231.19029275486-0.4232998423140.2264352635780.932753385983-0.4141034188961.11730259537-14.1486679613-29.2165003977-29.2901787734
125.71396712553.288839514321.68413718842.73898026198-0.08056854642034.725406853260.5726023650291.41173255919-0.813316629349-1.25680434697-0.05014111008960.9339210125640.691513266577-0.849922419806-0.4920077718920.909700813974-0.062098367508-0.2960293160561.45244876901-0.3653811463581.03064013295-24.8572907366-7.29930093417-52.1270826713
137.76479460127-2.1435559928-1.209001800273.68423495375-1.849432355941.755470743030.254055165551.43081400765-1.14379439926-0.344424831660.01629882002290.6697166935360.1121498786980.323324628845-0.2819569336030.700676260151-0.2041755418340.06710533573420.968504283727-0.2608031388790.674611350671-19.3431659745-11.9776660066-41.3904214529
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 100 )
2X-RAY DIFFRACTION2chain 'A' and (resid 101 through 416 )
3X-RAY DIFFRACTION3chain 'A' and (resid 417 through 498 )
4X-RAY DIFFRACTION4chain 'B' and (resid 8 through 169 )
5X-RAY DIFFRACTION5chain 'B' and (resid 170 through 276 )
6X-RAY DIFFRACTION6chain 'B' and (resid 277 through 416 )
7X-RAY DIFFRACTION7chain 'B' and (resid 417 through 498 )
8X-RAY DIFFRACTION8chain 'C' and (resid 11 through 197 )
9X-RAY DIFFRACTION9chain 'C' and (resid 198 through 276 )
10X-RAY DIFFRACTION10chain 'C' and (resid 277 through 351 )
11X-RAY DIFFRACTION11chain 'C' and (resid 352 through 416 )
12X-RAY DIFFRACTION12chain 'C' and (resid 417 through 463 )
13X-RAY DIFFRACTION13chain 'C' and (resid 464 through 498 )

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