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- PDB-5cab: Structure of Leishmania nucleoside diphostate kinase mutant Del5-Cterm -

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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 / CTP biosynthetic process / UTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / phosphorylation / 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-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

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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
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

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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

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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: 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

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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

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Phasing

PhasingMethod: molecular replacement

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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

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