[English] 日本語
Yorodumi
- PDB-5iom: Crystal Structure of Nucleoside Diphosphate Kinase from Schistoso... -

+
Open data


ID or keywords:

Loading...

-
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 / GTP biosynthetic process / nucleoside diphosphate kinase activity
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
Phasing

PhasingMethod: molecular replacement

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more