[English] 日本語
Yorodumi
- PDB-5cab: Structure of Leishmania nucleoside diphostate kinase mutant Del5-Cterm -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5cab
TitleStructure of Leishmania nucleoside diphostate kinase mutant Del5-Cterm
ComponentsNucleoside diphosphate kinase
KeywordsTRANSFERASE / Leishmania major / nucleoside diphosphate kinase / site directed-mutagenesis / quaternary structure / conformational stability
Function / homology
Function and homology information


nucleoside-diphosphate kinase / ciliary plasm / UTP biosynthetic process / CTP biosynthetic process / nucleoside diphosphate kinase activity / GTP biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase, active site / Nucleoside diphosphate kinase (NDPK) active site signature. / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase (NDPK)-like domain profile. / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily / Alpha-Beta Plaits ...Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase, active site / Nucleoside diphosphate kinase (NDPK) active site signature. / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase (NDPK)-like domain profile. / 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 speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.953 Å
AuthorsVieira, P.S. / de Giuseppe, P.O. / de Oliveira, A.H.C. / Murakami, M.T.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2011/24178-8 Brazil
Sao Paulo Research Foundation (FAPESP)10/51730-0 Brazil
CitationJournal: J.Struct.Biol. / Year: 2015
Title: The role of the C-terminus and Kpn loop in the quaternary structure stability of nucleoside diphosphate kinase from Leishmania parasites.
Authors: Vieira, P.S. / de Giuseppe, P.O. / de Oliveira, A.H. / Murakami, M.T.
History
DepositionJun 29, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2015Group: Database references
Revision 1.2Jan 17, 2018Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 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)36,6154
Polymers36,4232
Non-polymers1922
Water543
1
A: Nucleoside diphosphate kinase
B: Nucleoside diphosphate kinase
hetero molecules

A: Nucleoside diphosphate kinase
B: Nucleoside diphosphate kinase
hetero molecules

A: Nucleoside diphosphate kinase
B: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,84612
Polymers109,2706
Non-polymers5766
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area8780 Å2
ΔGint-46 kcal/mol
Surface area35390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.212, 113.212, 113.212
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and segid A
21chain B and segid B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and segid AA0
211chain B and segid BB0

-
Components

#1: Protein Nucleoside diphosphate kinase


Mass: 18211.666 Da / Num. of mol.: 2 / Fragment: UNP residues 1-146 / Mutation: Del5-Cterm
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Gene: L1648.07, LMJF_32_2950 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9U1E1, nucleoside-diphosphate kinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 3.47 Å3/Da / Density % sol: 64.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.33 / Details: ammonium sulfate, citric acid buffer

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.458 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.458 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 10372 / % possible obs: 99.2 % / Redundancy: 4.9 % / Biso Wilson estimate: 81.22 Å2 / Rmerge(I) obs: 0.081 / Χ2: 1.003 / Net I/av σ(I): 17.748 / Net I/σ(I): 10.8 / Num. measured all: 51126
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.95-3.063.10.6799531.00493.5
3.06-3.184.60.610171.00499.9
3.18-3.325.50.38510321.005100
3.32-3.55.60.21710441.001100
3.5-3.725.50.1410381.004100
3.72-45.30.09410411.002100
4-4.415.10.06810301.00499.8
4.41-5.044.90.05910581.004100
5.04-6.354.60.071056199.9
6.35-5050.03311031.00698.7

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
SCALEPACKdata scaling
MOLREP11.0.05phasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.15data extraction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NGS

3ngs


Resolution: 2.953→35.801 Å / FOM work R set: 0.7909 / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2657 495 4.78 %
Rwork0.2288 9852 -
obs0.2304 10347 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 148.59 Å2 / Biso mean: 75.78 Å2 / Biso min: 41.09 Å2
Refinement stepCycle: final / Resolution: 2.953→35.801 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2136 0 10 3 2149
Biso mean--102.81 53.32 -
Num. residues----277
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062190
X-RAY DIFFRACTIONf_angle_d1.1992958
X-RAY DIFFRACTIONf_chiral_restr0.053321
X-RAY DIFFRACTIONf_plane_restr0.006383
X-RAY DIFFRACTIONf_dihedral_angle_d13.89804
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1255X-RAY DIFFRACTION7.989TORSIONAL
12B1255X-RAY DIFFRACTION7.989TORSIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9528-3.24980.34681280.30062389X-RAY DIFFRACTION97
3.2498-3.71960.2941280.22342431X-RAY DIFFRACTION100
3.7196-4.68460.20871240.19662476X-RAY DIFFRACTION100
4.6846-100.28141150.23972556X-RAY DIFFRACTION99
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)
16.25660.2238-4.54629.17884.16032.0219-0.4741.7120.1577-1.2534-0.2251.7138-0.4861-1.2155-0.49221.2409-0.07810.27510.78640.19021.15116.278144.613412.245
24.531-0.74470.37463.3920.61844.4503-0.20550.31770.4051-0.01830.28840.4356-0.19840.5720.10640.3667-0.00560.03950.52890.16580.729421.642729.12865.9191
32.10760.22261.73117.12044.91527.69981.08780.41970.4383-0.2668-0.34250.3997-0.897-0.9391-0.56140.5831-0.2540.02761.25810.21220.997335.840737.9439-2.7029
41.25393.43830.19799.78391.49952.81-0.9620.36230.9271-1.0224-0.01520.9089-0.5403-0.4251-0.99690.8264-0.4540.04381.13670.14781.598842.90841.59674.4866
56.9389-3.6095.96533.2842-0.30872.03021.3294-1.9155-0.64920.8542-0.43431.00440.33620.3997-0.73140.9898-0.34310.32441.29680.19770.957642.331831.92481.387
60.88290.82641.41662.6091.23014.56970.25370.59690.4535-0.23940.34520.0277-0.61450.4036-0.56320.5543-0.04030.07410.61240.14630.836523.461534.90099.2343
73.46344.68881.42327.01571.77720.54211.067-0.3007-0.00611.2617-0.1801-0.09660.37220.0585-0.53060.5037-0.04540.07030.7293-0.00870.583831.225426.536518.0332
82.6063-0.00795.03926.80480.079.7832-0.11492.5850.7389-0.06210.0608-1.4463-0.05432.5357-0.04630.6492-0.0979-0.08120.69750.22940.70833.942124.756710.167
91.53781.05640.6274.12311.89461.71890.1739-0.49910.4252-0.65570.2575-0.6328-0.36690.0136-0.92790.7619-0.07030.27170.71370.2441.265127.591443.20647.4628
105.95293.4605-0.30215.8719-3.14822.2091-2.43581.51161.4808-0.50861.15931.1157-1.2206-0.10510.72021.3810.0061-0.09570.79860.20840.870319.576341.9746-2.5133
114.81370.2976-0.73993.16650.37341.9693-0.13770.46370.3049-0.12160.14910.34660.20020.61460.05370.43750.059-0.06590.66940.20240.518813.141222.4625-0.7556
128.38550.24566.33865.07442.05767.5626-0.40252.66421.9203-1.2601-0.5562-0.5434-0.9747-0.87490.32890.67560.23090.03731.46620.48150.76761.948635.2773-8.6517
133.06472.1257-1.45678.0635-1.15811.98610.8810.9774-0.90610.817-0.4714-0.27430.26440.9851-0.25360.54640.1848-0.07891.42270.22230.8706-6.365129.9101-8.0355
143.4749-2.4084-0.25363.79612.93093.3786-0.79350.4504-0.0441-0.60670.38260.9196-0.16110.66320.01160.5005-0.12820.04060.86970.18230.575213.658624.0975-4.926
152.4586-2.8108-2.67283.55153.19282.94680.46470.892-0.22080.66081.5390.09981.12630.7899-1.80910.853-0.0869-0.03840.98510.02690.547610.637412.3182-7.6029
166.0506-2.7421-1.1167.16260.84118.85030.1859-0.3599-1.3925-0.1769-0.09380.5241-0.8471-1.0349-0.0650.4837-0.0279-0.09050.59670.03840.59761.698514.3384-0.0102
171.2641.55112.62644.70914.64826.33460.62290.09380.01680.9194-0.3729-0.52972.3525-0.23740.06550.5673-0.03880.07180.4865-0.04090.80222.67712.86164.8385
184.35981.67190.16174.7288-0.21423.2953-0.30470.63721.0429-0.65040.26891.2978-0.4299-0.06440.38050.60120.0477-0.09350.73790.20210.78141.379220.5545-1.249
199.3075-3.94112.19265.81964.0366.44120.06790.9228-0.9503-1.1209-0.86470.7486-0.634-0.68950.0590.59130.1203-0.06071.55180.30160.59758.348622.9843-15.6204
203.4613-1.7498-0.04932.00514.90732.4783-0.85392.48440.7691-1.42061.2055-2.0591-0.55940.0117-0.19251.2208-0.160.22661.4980.49960.982215.150731.2854-12.6798
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:6)A1 - 6
2X-RAY DIFFRACTION2(chain A and resid 7:42)A7 - 42
3X-RAY DIFFRACTION3(chain A and resid 43:51)A43 - 51
4X-RAY DIFFRACTION4(chain A and resid 52:57)A52 - 57
5X-RAY DIFFRACTION5(chain A and resid 58:66)A58 - 66
6X-RAY DIFFRACTION6(chain A and resid 67:90)A67 - 90
7X-RAY DIFFRACTION7(chain A and resid 91:106)A91 - 106
8X-RAY DIFFRACTION8(chain A and resid 107:116)A107 - 116
9X-RAY DIFFRACTION9(chain A and resid 117:131)A117 - 131
10X-RAY DIFFRACTION10(chain A and resid 132:139)A132 - 139
11X-RAY DIFFRACTION11(chain B and resid 2:39)B2 - 39
12X-RAY DIFFRACTION12(chain B and resid 40:50)B40 - 50
13X-RAY DIFFRACTION13(chain B and resid 51:69)B51 - 69
14X-RAY DIFFRACTION14(chain B and resid 70:80)B70 - 80
15X-RAY DIFFRACTION15(chain B and resid 81:87)B81 - 87
16X-RAY DIFFRACTION16(chain B and resid 88:96)B88 - 96
17X-RAY DIFFRACTION17(chain B and resid 97:106)B97 - 106
18X-RAY DIFFRACTION18(chain B and resid 107:122)B107 - 122
19X-RAY DIFFRACTION19(chain B and resid 123:130)B123 - 130
20X-RAY DIFFRACTION20(chain B and resid 131:139)B131 - 139

+
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