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- PDB-5c7p: Structure of Leishmania nucleoside diphostate kinase mutant P95S -

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Basic information

Entry
Database: PDB / ID: 5c7p
TitleStructure of Leishmania nucleoside diphostate kinase mutant P95S
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 / Resolution: 3.144 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 24, 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
C: Nucleoside diphosphate kinase


Theoretical massNumber of molelcules
Total (without water)56,4673
Polymers56,4673
Non-polymers00
Water00
1
A: Nucleoside diphosphate kinase
B: Nucleoside diphosphate kinase
C: Nucleoside diphosphate kinase

A: Nucleoside diphosphate kinase
B: Nucleoside diphosphate kinase
C: Nucleoside diphosphate kinase


Theoretical massNumber of molelcules
Total (without water)112,9346
Polymers112,9346
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area14460 Å2
ΔGint-57 kcal/mol
Surface area34650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.191, 113.191, 95.243
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and segid A
21chain B and segid B
31chain C and segid C

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and segid AA0
211chain B and segid BB0
311chain C and segid CC0

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Components

#1: Protein Nucleoside diphosphate kinase


Mass: 18822.283 Da / Num. of mol.: 3 / Mutation: P95S
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

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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: 3.12 Å3/Da / Density % sol: 60.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 1.4 mol.L-1 tri-sodium citrate pH 6.0

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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: Aug 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.458 Å / Relative weight: 1
ReflectionResolution: 3.144→40 Å / Num. obs: 12356 / % possible obs: 98 % / Redundancy: 4.4 % / Biso Wilson estimate: 58.21 Å2 / Rmerge(I) obs: 0.158 / Χ2: 0.974 / Net I/av σ(I): 9.039 / Net I/σ(I): 5 / Num. measured all: 54462
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3.144-3.264.30.66712270.85599.6
3.26-3.394.60.49112410.86299.9
3.39-3.554.60.31712530.928100
3.55-3.734.60.24812310.946100
3.73-3.974.60.17912491.00199.8
3.97-4.274.50.12912351.05299.3
4.27-4.74.40.1112371.03798
4.7-5.384.40.1212081.00595.4
5.38-6.784.10.15912111.05494.6
6.78-4040.07712641.02293.5

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALEPACKdata scaling
MOLREP11.1.03phasing
PDB_EXTRACT3.15data extraction
DENZOdata reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NGS

3ngs


Resolution: 3.144→34.155 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2533 599 4.86 %
Rwork0.1996 11721 -
obs0.2022 12320 97.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 151.75 Å2 / Biso mean: 60.5249 Å2 / Biso min: 23.94 Å2
Refinement stepCycle: final / Resolution: 3.144→34.155 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3384 0 0 0 3384
Num. residues----434
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053459
X-RAY DIFFRACTIONf_angle_d0.9684667
X-RAY DIFFRACTIONf_chiral_restr0.042506
X-RAY DIFFRACTIONf_plane_restr0.005597
X-RAY DIFFRACTIONf_dihedral_angle_d14.1161258
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1955X-RAY DIFFRACTION7.012TORSIONAL
12B1955X-RAY DIFFRACTION7.012TORSIONAL
13C1955X-RAY DIFFRACTION7.012TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1439-3.460.25771660.223329273093100
3.46-3.960.22161470.176629523099100
3.96-4.98680.23591450.17032932307798
4.9868-34.15690.29261410.23312910305194
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)
12.7227-1.18590.09262.5717-0.60262.03480.0061-0.2834-0.43350.0739-0.0135-0.25390.35710.1786-0.06450.34240.0754-0.01710.31470.05380.4343-8.3722-52.34999.6098
22.84970.1278-0.40232.91550.57453.20440.0926-0.7201-0.26860.4451-0.1190.158-0.1646-0.14810.00720.3640.0090.07440.50620.09080.2673-28.0442-44.577119.7308
32.0291-0.8973-0.8943.3130.52531.56550.0062-0.12050.35880.2470.11220.1521-0.43020.0215-0.02080.42130.0096-0.00330.2757-0.05860.4486-18.6537-14.15927.1697
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 2:150)A2 - 150
2X-RAY DIFFRACTION2(chain B and resid 2:151)B2 - 151
3X-RAY DIFFRACTION3(chain C and resid 1:150)C1 - 150

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