[English] 日本語
Yorodumi
- PDB-5kk8: Crystal structure of Nucleoside Diphosphate Kinase from Schistoso... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5kk8
TitleCrystal structure of Nucleoside Diphosphate Kinase from Schistosoma mansoni in complex with ADP
ComponentsNucleoside diphosphate kinase
KeywordsTRANSFERASE / Nucleoside Diphosphate Kinase / enzyme
Function / homology
Function and homology information


nucleoside-diphosphate kinase / CTP biosynthetic process / UTP 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
ADENOSINE-5'-DIPHOSPHATE / Nucleoside diphosphate kinase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.11 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, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2012/14223-9 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
DepositionJun 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6454
Polymers33,7912
Non-polymers8542
Water3,315184
1
A: Nucleoside diphosphate kinase
hetero molecules

A: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6454
Polymers33,7912
Non-polymers8542
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_755-x+y+2,y,-z+1/21
Buried area3440 Å2
ΔGint-22 kcal/mol
Surface area14610 Å2
MethodPISA
2
B: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3232
Polymers16,8951
Non-polymers4271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area710 Å2
ΔGint-5 kcal/mol
Surface area8120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.450, 71.450, 219.340
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-302-

HOH

21A-416-

HOH

31A-421-

HOH

41A-422-

HOH

51B-361-

HOH

61B-362-

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 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G4VJY9, nucleoside-diphosphate kinase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 48.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 10% (w/v) PEG-8000, 100mM Tris pH 7.0, 200mM MgCl2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / 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: 2.11→61.88 Å / Num. obs: 20075 / % possible obs: 100 % / Redundancy: 18.9 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 27.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.11-2.1619.60.711100
9.44-61.8814.50.027199.4

-
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: 5IOM

5iom


Resolution: 2.11→59.553 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.04
RfactorNum. reflection% reflection
Rfree0.1987 1020 5.09 %
Rwork0.1682 --
obs0.1697 20023 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 111.7 Å2 / Biso mean: 36.2823 Å2 / Biso min: 15.72 Å2
Refinement stepCycle: final / Resolution: 2.11→59.553 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2342 0 54 184 2580
Biso mean--79.74 41.85 -
Num. residues----298
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072466
X-RAY DIFFRACTIONf_angle_d0.9623342
X-RAY DIFFRACTIONf_chiral_restr0.051355
X-RAY DIFFRACTIONf_plane_restr0.005426
X-RAY DIFFRACTIONf_dihedral_angle_d17.8481482
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.1101-2.22130.23531300.177926502780
2.2213-2.36050.20571520.175426102762
2.3605-2.54270.2211450.181226692814
2.5427-2.79860.22681580.179126442802
2.7986-3.20360.21231450.172927012846
3.2036-4.0360.19941270.152527712898
4.036-59.57680.17061630.168429583121
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)
11.2559-0.1179-0.03170.4255-0.14061.40090.07340.0368-0.1113-0.0444-0.0264-0.01780.0336-0.1155-0.0180.17320.0051-0.00610.1571-0.01050.227473.213107.876847.5305
21.5376-0.21770.14340.7266-0.45421.92690.00640.1149-0.1411-0.0946-0.055-0.01560.25820.10230.02410.2356-0.0056-0.02440.1525-0.02550.26477.840199.653842.6272
35.16062.19650.29642.9052-0.18173.3431-0.1760.72310.2991-0.6530.0220.18930.0353-0.1933-0.03150.27580.0001-0.05810.2641-0.01920.253665.1425110.582737.5554
40.93070.2260.12980.813-0.04811.64660.01520.1487-0.0172-0.18750.01630.0118-0.0484-0.0724-0.01020.1870.0135-0.00090.1893-0.04190.243876.3394108.135638.8497
52.2778-1.6232-0.41942.16660.42580.96880.0754-0.0565-0.4477-0.2329-0.01550.54120.0308-0.0581-0.05940.2673-0.048-0.05360.2434-0.02380.332356.7262103.080748.7295
60.90560.0262-0.1490.94930.08921.49470.07530.1833-0.04450.13020.0163-0.13860.14530.1335-0.02020.44310.0244-0.05270.3932-0.02520.220880.1159109.69226.6456
70.9726-0.1963-1.21410.7456-0.02883.2037-0.1201-0.0281-0.38630.1645-0.0261-0.02020.76710.07360.04760.65050.0439-0.07940.3637-0.04120.323876.138493.281717.9372
80.35960.18790.07291.1682-0.28332.10280.15860.4154-0.1110.25940.01010.05220.0733-0.1611-0.03830.49080.0298-0.02610.3761-0.02550.281375.404699.033610.8548
96.6603-1.54280.65532.02420.6485.05110.1972-0.2695-0.12940.5092-0.1646-0.39610.34140.3178-0.0310.4253-0.0096-0.04540.40640.01550.189883.6696115.243416.8949
100.9811-0.2144-0.02270.6304-0.35691.8360.13630.0151-0.0450.2269-0.0041-0.05130.0585-0.0945-0.01130.4531-0.0105-0.04110.3640.02680.256875.1017107.737215.9394
110.80230.8213-0.22392.7471-0.59671.24370.135-0.12870.12980.3473-0.03-0.10130.070.1591-0.03250.48660.0263-0.04330.6245-0.05820.298894.3587113.58056.1898
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 26 )A1 - 26
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 76 )A27 - 76
3X-RAY DIFFRACTION3chain 'A' and (resid 77 through 88 )A77 - 88
4X-RAY DIFFRACTION4chain 'A' and (resid 89 through 130 )A89 - 130
5X-RAY DIFFRACTION5chain 'A' and (resid 131 through 149 )A131 - 149
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 38 )B1 - 38
7X-RAY DIFFRACTION7chain 'B' and (resid 39 through 57 )B39 - 57
8X-RAY DIFFRACTION8chain 'B' and (resid 58 through 76 )B58 - 76
9X-RAY DIFFRACTION9chain 'B' and (resid 77 through 88 )B77 - 88
10X-RAY DIFFRACTION10chain 'B' and (resid 89 through 130 )B89 - 130
11X-RAY DIFFRACTION11chain 'B' and (resid 131 through 149 )B131 - 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://pdbjlvh1.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