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- PDB-7mk0: Trypanosoma cruzi Nucleoside Diphosphate Kinase 1 form a quinary ... -

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Basic information

Entry
Database: PDB / ID: 7mk0
TitleTrypanosoma cruzi Nucleoside Diphosphate Kinase 1 form a quinary multihexameric structure
ComponentsNucleoside diphosphate kinase
KeywordsTRANSFERASE / Kinase / cruzi / ndpk1
Function / homology
Function and homology information


nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / nucleoside diphosphate kinase activity / GTP biosynthetic process / ATP binding
Similarity search - Function
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
Similarity search - Domain/homology
Nucleoside diphosphate kinase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsGomez, J.A. / Aguilar, C.F.
Funding support Brazil, Argentina, 2items
OrganizationGrant numberCountry
Coordination for the Improvement of Higher Education Personnel Brazil
Agencia Nacional de Promocion Cientifica y Tecnologica (FONCYT) Argentina
Citation
Journal: Acta Crystallogr D Struct Biol / Year: 2022
Title: X-ray diffraction and in vivo studies reveal the quinary structure of Trypanosoma cruzi nucleoside diphosphate kinase 1: a novel helical oligomer structure.
Authors: Gomez Barroso, J.A. / Miranda, M.R. / Pereira, C.A. / Garratt, R.C. / Aguilar, C.F.
#1: Journal: Acta Crystallographica Section F Structural Biology and Crystallization Communications
Year: 2010
Title: Protein preparation, crystallization and preliminary X-ray analysis of Trypanosoma cruzi nucleoside diphosphate kinase 1
Authors: Gomez, J.A. / Aguilar, C.F.
History
DepositionApr 21, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleoside diphosphate kinase
B: Nucleoside diphosphate kinase
C: Nucleoside diphosphate kinase
D: Nucleoside diphosphate kinase
E: Nucleoside diphosphate kinase
F: Nucleoside diphosphate kinase
G: Nucleoside diphosphate kinase
H: Nucleoside diphosphate kinase
I: Nucleoside diphosphate kinase
J: Nucleoside diphosphate kinase
K: Nucleoside diphosphate kinase
L: Nucleoside diphosphate kinase
M: Nucleoside diphosphate kinase
N: Nucleoside diphosphate kinase
O: Nucleoside diphosphate kinase
P: Nucleoside diphosphate kinase
Q: Nucleoside diphosphate kinase
R: Nucleoside diphosphate kinase
S: Nucleoside diphosphate kinase
T: Nucleoside diphosphate kinase
U: Nucleoside diphosphate kinase
V: Nucleoside diphosphate kinase
W: Nucleoside diphosphate kinase
X: Nucleoside diphosphate kinase


Theoretical massNumber of molelcules
Total (without water)401,81224
Polymers401,81224
Non-polymers00
Water00
1
A: Nucleoside diphosphate kinase
B: Nucleoside diphosphate kinase
C: Nucleoside diphosphate kinase
D: Nucleoside diphosphate kinase
E: Nucleoside diphosphate kinase
F: Nucleoside diphosphate kinase


Theoretical massNumber of molelcules
Total (without water)100,4536
Polymers100,4536
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15550 Å2
ΔGint-68 kcal/mol
Surface area35480 Å2
MethodPISA
2
G: Nucleoside diphosphate kinase
H: Nucleoside diphosphate kinase
I: Nucleoside diphosphate kinase
J: Nucleoside diphosphate kinase
K: Nucleoside diphosphate kinase
L: Nucleoside diphosphate kinase


Theoretical massNumber of molelcules
Total (without water)100,4536
Polymers100,4536
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16680 Å2
ΔGint-72 kcal/mol
Surface area34570 Å2
MethodPISA
3
M: Nucleoside diphosphate kinase
N: Nucleoside diphosphate kinase
O: Nucleoside diphosphate kinase
P: Nucleoside diphosphate kinase
Q: Nucleoside diphosphate kinase
R: Nucleoside diphosphate kinase


Theoretical massNumber of molelcules
Total (without water)100,4536
Polymers100,4536
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16170 Å2
ΔGint-73 kcal/mol
Surface area35590 Å2
MethodPISA
4
S: Nucleoside diphosphate kinase
T: Nucleoside diphosphate kinase
U: Nucleoside diphosphate kinase
V: Nucleoside diphosphate kinase
W: Nucleoside diphosphate kinase
X: Nucleoside diphosphate kinase


Theoretical massNumber of molelcules
Total (without water)100,4536
Polymers100,4536
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16220 Å2
ΔGint-76 kcal/mol
Surface area35200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.842, 127.842, 275.494
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number143
Space group name H-MP3

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Components

#1: Protein ...
Nucleoside diphosphate kinase


Mass: 16742.168 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: C3747_234g48, C3747_68g44, C4B63_80g21 / Plasmid: pRSET-A / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A2V2WVR0, 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: 3.23 Å3/Da / Density % sol: 61.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.3 / Details: PEG3350 20% Magnesium chloride 200mM

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.45 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 30, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.291
11-K, -H, -L20.237
11K, H, -L30.24
11-h,-k,l40.232
ReflectionResolution: 3→86.38 Å / Num. obs: 58612 / % possible obs: 92.3 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.34 / Net I/σ(I): 2.7
Reflection shellResolution: 3.498→3.69 Å / Rmerge(I) obs: 1.121 / Num. unique obs: 9287 / % possible all: 99.9

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Processing

Software
NameVersionClassification
SCALA5.6.0117data scaling
REFMAC5.6.0117refinement
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BBC

3bbc


Resolution: 3.5→10 Å / Cor.coef. Fo:Fc: 0.432 / Cor.coef. Fo:Fc free: 0.387 / SU B: 11.722 / SU ML: 0.199 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.143 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2777 3266 5.4 %RANDOM
Rwork0.2686 ---
obs0.2691 57214 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 275.14 Å2 / Biso mean: 15.659 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-2.76 Å20 Å20 Å2
2--2.76 Å20 Å2
3----5.52 Å2
Refinement stepCycle: final / Resolution: 3.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28296 0 0 0 28296
Num. residues----3624
LS refinement shellResolution: 3.5→3.577 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.227 254 -
Rwork0.192 3794 -
obs--96.68 %

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