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- PDB-3r9l: Crystal structure of nucleoside diphosphate kinase from Giardia l... -

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Basic information

Entry
Database: PDB / ID: 3r9l
TitleCrystal structure of nucleoside diphosphate kinase from Giardia lamblia featuring a disordered dinucleotide binding site
ComponentsNucleoside diphosphate kinase
KeywordsTRANSFERASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / giardiasis / intestinal disease / protozoan parasite / water contaminant / kinase / phosphoryltransfer / ADP
Function / homology
Function and homology information


nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / ATP binding
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
nucleoside-diphosphate kinase
Similarity search - Component
Biological speciesGiardia lamblia (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.65 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of nucleoside diphosphate kinase from Giardia lamblia featuring a disordered dinucleotide binding site
Authors: Edwards, T.E. / Gardberg, A.S. / Sankaran, B. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionMar 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1502
Polymers17,1151
Non-polymers351
Water23413
1
A: Nucleoside diphosphate kinase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)102,90112
Polymers102,6886
Non-polymers2136
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
crystal symmetry operation10_554-y,-x,-z-1/21
crystal symmetry operation11_654-x+y+1,y,-z-1/21
crystal symmetry operation12_544x,x-y-1,-z-1/21
Buried area8950 Å2
ΔGint-83 kcal/mol
Surface area26860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.960, 116.960, 62.690
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Nucleoside diphosphate kinase


Mass: 17114.713 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Giardia lamblia (eukaryote) / Strain: ATCC 50803 / WB clone C6 / Gene: GL50803_11301 / Production host: Escherichia coli (E. coli) / References: UniProt: A8BMG9, nucleoside-diphosphate kinase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 3.62 Å3/Da / Density % sol: 65.99 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.9
Details: GilaA.00438.a.A1 PW27083 at 24.97 mg/mL in 25 mM Hepes pH 7.0, 0.5 M NaCl, 5% glycerol, 2 mM DTT, 0.025% azide against CSHT C11 focus screen 0.1 M Hepes pH 7.0, 0.9 M Na phosphate, 0.9 M K ...Details: GilaA.00438.a.A1 PW27083 at 24.97 mg/mL in 25 mM Hepes pH 7.0, 0.5 M NaCl, 5% glycerol, 2 mM DTT, 0.025% azide against CSHT C11 focus screen 0.1 M Hepes pH 7.0, 0.9 M Na phosphate, 0.9 M K phosphate with 25% ethylene glycol as cryo-protectant, crystal tracking ID 216300h9, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. all: 7760 / Num. obs: 7665 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 60.858 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 26.02
Reflection shell
Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
2.65-2.7260.5263.263384567567100
2.72-2.790.4313.92308452099.8
2.79-2.870.3724.633232541100
2.87-2.960.2755.953005509100
2.96-3.060.1769.18287649499.8
3.06-3.170.156102936496100
3.17-3.290.13312.46273946199.8
3.29-3.420.08918.532634452100
3.42-3.570.06324.51251243599.5
3.57-3.750.05229.59244641899.5
3.75-3.950.03836.71230139599
3.95-4.190.03145.05218137998.4
4.19-4.480.02948.62196035199.2
4.48-4.840.02654.42182733398.2
4.84-5.30.02850.25169830797.8
5.3-5.930.02849.45149627095.7
5.93-6.840.02553.16136125296.9
6.84-8.380.01764.97120221494.7
8.38-11.850.01376.0992516993.4
11.850.01175.249510285

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 48.98 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.68 Å42.07 Å
Translation2.68 Å42.07 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
BOSdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NPK

1npk


Resolution: 2.65→39.4 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.907 / WRfactor Rfree: 0.2439 / WRfactor Rwork: 0.2196 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8203 / SU B: 18.006 / SU ML: 0.172 / SU R Cruickshank DPI: 0.2899 / SU Rfree: 0.2432 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2663 348 4.6 %RANDOM
Rwork0.2344 ---
obs0.2359 7619 98.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 167.8 Å2 / Biso mean: 78.7938 Å2 / Biso min: 9.45 Å2
Baniso -1Baniso -2Baniso -3
1-1.33 Å20.67 Å20 Å2
2--1.33 Å20 Å2
3----2 Å2
Refinement stepCycle: LAST / Resolution: 2.65→39.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms813 0 1 13 827
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022827
X-RAY DIFFRACTIONr_angle_refined_deg1.2781.9481120
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8115110
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.36122.18832
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.31315123
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.396158
X-RAY DIFFRACTIONr_chiral_restr0.0830.2128
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021628
X-RAY DIFFRACTIONr_mcbond_it0.8541.5551
X-RAY DIFFRACTIONr_mcangle_it1.5712871
X-RAY DIFFRACTIONr_scbond_it1.5393276
X-RAY DIFFRACTIONr_scangle_it2.6954.5249
LS refinement shellResolution: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 22 -
Rwork0.324 540 -
all-562 -
obs--99.47 %
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)
1-0.1892-0.45091.4067-1.4193-2.71189.5645-0.6114-0.13490.23060.0468-0.136-0.62380.7019-1.20750.74740.5665-0.4438-0.06050.50120.19550.276242.5508-49.7868-2.2016
21.00210.55580.27850.3253-0.17922.2016-0.01-0.10770.05310.033-0.0741-0.04430.0587-0.3640.08410.0732-0.07540.00940.1726-0.00430.11945.5237-39.3486-5.7882
31.4323-0.4106-0.4175-1.32432.46043.0736-0.0248-0.34650.5661-0.0106-0.02390.1407-0.4427-0.37670.04880.1763-0.03420.0610.3647-0.08350.309741.3597-35.2567-0.3983
412.81911.81834.83623.83050.2214-5.66081.0619-0.81410.55120.545-1.01130.60650.7726-0.341-0.05070.3326-0.4470.16640.52380.00130.042533.6002-50.3939-4.55
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 9
2X-RAY DIFFRACTION2A10 - 106
3X-RAY DIFFRACTION3A107 - 123
4X-RAY DIFFRACTION4A124 - 139

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