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- PDB-5iom: Crystal Structure of Nucleoside Diphosphate Kinase from Schistoso... -

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Basic information

Entry
Database: PDB / ID: 5iom
TitleCrystal Structure of Nucleoside Diphosphate Kinase from Schistosoma mansoni is space group P6322
ComponentsNucleoside diphosphate kinase
KeywordsTRANSFERASE / Nucleoside Diphosphate Kinase / enzyme
Function / homology
Function and homology information


nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / nucleoside diphosphate kinase activity / GTP biosynthetic process
Similarity search - Function
Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Nucleoside diphosphate kinase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsTorini, J.R.S. / Romanello, L. / Bird, L.E. / Nettleship, J.E. / Owens, R.J. / Aller, P. / DeMarco, R. / Brandao-Neto, J. / Pereira, H.M.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2012/14223-9 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)474402/2013-4 Brazil
CitationJournal: Mol.Biochem.Parasitol. / Year: 2019
Title: Characterization of a Schistosoma mansoni NDPK expressed in sexual and digestive organs.
Authors: Torini, J.R. / de Freitas Fernandes, A. / Balasco Serrao, V.H. / Romanello, L. / Bird, L.E. / Nettleship, J.E. / Owens, R.J. / Brandao-Neto, J. / Zeraik, A.E. / DeMarco, R. / D'Muniz Pereira, H.
History
DepositionMar 8, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2May 29, 2019Group: Data collection / 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoside diphosphate kinase
B: Nucleoside diphosphate kinase


Theoretical massNumber of molelcules
Total (without water)33,7912
Polymers33,7912
Non-polymers00
Water6,179343
1
A: Nucleoside diphosphate kinase
x 6


Theoretical massNumber of molelcules
Total (without water)101,3726
Polymers101,3726
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation10_554-y,-x,-z-1/21
crystal symmetry operation11_554-x+y,y,-z-1/21
crystal symmetry operation12_554x,x-y,-z-1/21
Buried area17780 Å2
ΔGint-79 kcal/mol
Surface area33200 Å2
MethodPISA
2
B: Nucleoside diphosphate kinase
x 6


Theoretical massNumber of molelcules
Total (without water)101,3726
Polymers101,3726
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation9_555-x,-x+y,-z1
Buried area17650 Å2
ΔGint-74 kcal/mol
Surface area33160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.590, 71.590, 219.440
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-204-

HOH

21A-379-

HOH

31B-202-

HOH

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Components

#1: Protein Nucleoside diphosphate kinase


Mass: 16895.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Gene: Smp_092750 / Plasmid: pOPINF / Production host: Escherichia coli (E. coli) / Strain (production host): Lemo21 / References: UniProt: G4VJY9, nucleoside-diphosphate kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / 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: 2.4 Å3/Da / Density % sol: 48.79 % / Description: hexagonal needles
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10% PEG 20 000, 20% v/v PEG MME 550, 100mM MES/imidazole pH 6.5, 20mM of each 1,6-hexanediol, 1-butanol,(RS)-1,2- propanediol, 2-propanol, 1,4-butanediol and 1,3-propanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.9→47.3 Å / Num. obs: 27155 / % possible obs: 99.6 % / Redundancy: 9.6 % / Biso Wilson estimate: 23.07 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.104 / Net I/σ(I): 15.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.9-1.95100.7043.6199.5
8.5-47.380.04135.7198.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
xia2data scaling
PHASERphasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IOL

5iol


Resolution: 1.9→47.295 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.46
RfactorNum. reflection% reflectionSelection details
Rfree0.2077 1361 5.02 %random selection
Rwork0.1621 ---
obs0.1644 27125 99.42 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 75.47 Å2 / Biso mean: 28.1872 Å2 / Biso min: 9.98 Å2
Refinement stepCycle: final / Resolution: 1.9→47.295 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2362 0 0 343 2705
Biso mean---38.08 -
Num. residues----299
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112428
X-RAY DIFFRACTIONf_angle_d1.0233280
X-RAY DIFFRACTIONf_chiral_restr0.064349
X-RAY DIFFRACTIONf_plane_restr0.007429
X-RAY DIFFRACTIONf_dihedral_angle_d16.8691477
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.9680.28371190.22742515263499
1.968-2.04670.25611400.20632477261798
2.0467-2.13990.19031360.1732496263299
2.1399-2.25270.20061280.165225452673100
2.2527-2.39390.23571480.168125272675100
2.3939-2.57870.24581540.16425382692100
2.5787-2.83810.20051380.163525602698100
2.8381-3.24870.20871410.16762590273199
3.2487-4.09270.1841180.144326642782100
4.0927-47.310.18881390.14922852299199
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)
13.7669-0.14151.06390.8598-0.31541.98570.04240.0061-0.018-0.0199-0.0304-0.07940.05090.1358-0.01920.10820.00480.00620.07090.00040.14961.1378-16.0258-47.3954
21.38620.4045-1.1140.6242-1.27855.93490.075-0.1568-0.0906-0.16050.07810.19170.4888-0.1487-0.07260.1945-0.022-0.02370.09790.02210.2105-10.1642-28.6628-39.3342
32.89661.4098-1.12363.9778-3.66913.4020.2218-0.20840.13310.1590.21710.3303-0.0218-0.2236-0.36570.1339-0.0267-0.00220.13410.02810.212-15.3041-24.6057-42.3423
40.56071.02020.24614.64931.64714.84960.03420.0086-0.22040.11750.0917-0.3590.08340.374-0.16510.15660.0276-0.01210.09510.05780.18736.8433-19.0382-44.4835
53.867-5.6948-1.80728.3642.37831.8111-0.3973-0.5663-0.44320.35350.26920.85740.0404-0.11450.11010.1947-0.0020.00630.20530.02010.2499-1.4299-11.1537-36.3976
68.903-0.4071-2.83671.9971-1.88266.85340.4286-0.40960.6391-0.0521-0.13420.1077-0.55110.3067-0.23420.1636-0.02110.02460.1413-0.00750.2587-5.4058-5.5309-41.6343
72.4221-0.78880.66862.2704-0.54461.64720.0536-0.2135-0.02910.1030.059-0.03050.0306-0.0229-0.14620.1085-0.00230.00630.10430.01490.1279-3.6316-21.0807-39.0203
83.84713.4411-4.12223.0878-3.61824.3218-0.2091-0.1013-1.0091-0.1411-0.0482-0.72930.25740.20070.27990.21460.0795-0.01210.2244-0.00250.306610.3495-27.2248-50.2553
96.49080.86550.93356.17652.64722.97830.1386-0.2314-0.35370.49180.0626-0.02190.60870.5032-0.1780.17830.03540.00370.14590.00650.261820.9408-11.2684-46.7464
106.1113-0.17360.70931.7824-0.17311.3223-0.1002-0.0746-0.1091-0.10940.05210.11620.1751-0.21710.04720.28540.0147-0.00650.2883-0.00880.1343-6.1253-17.6478-8.6441
119.206-5.7931.74023.8276-0.64932.1092-0.091-0.42320.69240.51040.1464-0.0796-0.31080.0094-0.06690.2792-0.03040.02970.2647-0.00520.1871-7.1458-8.4945-4.9297
120.87-1.0116-0.23753.3662-1.24311.07510.01480.0501-0.0310.1042-0.01260.11840.0362-0.0085-0.06460.3482-0.0252-0.02330.3511-0.01190.1596-13.6975-15.3305-5.5268
132.6693-0.6554-3.22490.95540.22417.95730.00830.0644-0.23560.12080.00040.08220.37-0.00040.12510.394-0.0405-0.02170.2413-0.02760.2502-4.9177-30.682-17.8347
141.9634-1.1045-0.0862.62550.79662.0836-0.0277-0.06170.00010.2074-0.03430.00230.1107-0.01620.08970.2207-0.041-0.00770.20560.00280.1447-6.1469-22.1075-11.5953
158.53421.44430.52451.16160.0441.007-0.01210.9587-0.5217-0.078-0.014-0.26320.04770.21120.01150.39710.0142-0.01640.3901-0.01260.1818-4.378-10.4521-18.4376
164.3142-0.24150.64231.56950.02171.758-0.0261-0.07130.1233-0.18910.1391-0.06680.02440.0248-0.0950.3411-0.00180.01420.2843-0.02280.17010.8783-13.2534-14.3891
173.5425-1.67982.87486.4722-4.0339.47810.05090.23040.1519-0.4427-0.33350.28210.6655-0.61230.25110.3134-0.0056-0.00210.3384-0.03520.1641-15.8642-22.818-16.763
181.8872-2.2594-1.88383.64023.56213.75880.08490.2029-0.43030.1797-0.22870.4340.0058-0.87580.16280.40240.02730.01890.54110.02550.1519-22.6947-18.417-4.5018
196.274-1.27580.64415.6698-3.72872.4588-0.21460.1921-0.1627-1.12-0.03520.67560.5102-0.23870.11140.4556-0.0596-0.05470.3862-0.02390.245-23.60890.6476-8.0948
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 35 )A0 - 35
2X-RAY DIFFRACTION2chain 'A' and (resid 36 through 57 )A36 - 57
3X-RAY DIFFRACTION3chain 'A' and (resid 58 through 70 )A58 - 70
4X-RAY DIFFRACTION4chain 'A' and (resid 71 through 79 )A71 - 79
5X-RAY DIFFRACTION5chain 'A' and (resid 80 through 95 )A80 - 95
6X-RAY DIFFRACTION6chain 'A' and (resid 96 through 105 )A96 - 105
7X-RAY DIFFRACTION7chain 'A' and (resid 106 through 130 )A106 - 130
8X-RAY DIFFRACTION8chain 'A' and (resid 131 through 141 )A131 - 141
9X-RAY DIFFRACTION9chain 'A' and (resid 142 through 149 )A142 - 149
10X-RAY DIFFRACTION10chain 'B' and (resid 1 through 17 )B1 - 17
11X-RAY DIFFRACTION11chain 'B' and (resid 18 through 27 )B18 - 27
12X-RAY DIFFRACTION12chain 'B' and (resid 28 through 38 )B28 - 38
13X-RAY DIFFRACTION13chain 'B' and (resid 39 through 57 )B39 - 57
14X-RAY DIFFRACTION14chain 'B' and (resid 58 through 79 )B58 - 79
15X-RAY DIFFRACTION15chain 'B' and (resid 80 through 95 )B80 - 95
16X-RAY DIFFRACTION16chain 'B' and (resid 96 through 119 )B96 - 119
17X-RAY DIFFRACTION17chain 'B' and (resid 120 through 130 )B120 - 130
18X-RAY DIFFRACTION18chain 'B' and (resid 131 through 141 )B131 - 141
19X-RAY DIFFRACTION19chain 'B' and (resid 142 through 149 )B142 - 149

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