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- PDB-4fkx: Crystal structure of nucleoside diphosphate kinase B from Trypano... -

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Basic information

Entry
Database: PDB / ID: 4fkx
TitleCrystal structure of nucleoside diphosphate kinase B from Trypanosoma brucei bound to CDP
ComponentsNucleoside diphosphate kinaseNucleoside-diphosphate kinase
KeywordsTRANSFERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / NTP biosynthesis / NDP / African trypanosomiasis / African sleeping sickness
Function / homology
Function and homology information


nucleoside-diphosphate kinase / UTP biosynthetic process / ciliary plasm / CTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / post-transcriptional regulation of gene expression / phosphorylation / ATP binding / nucleus / 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
CYTIDINE-5'-DIPHOSPHATE / Nucleoside diphosphate kinase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of nucleoside diphosphate kinase B from Trypanosoma brucei bound to CDP
Authors: Gardberg, A.S. / Edwards, T.E. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionJun 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 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 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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
B: Nucleoside diphosphate kinase
C: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,13210
Polymers53,7313
Non-polymers1,4017
Water9,296516
1
A: Nucleoside diphosphate kinase
B: Nucleoside diphosphate kinase
C: Nucleoside diphosphate kinase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)110,26420
Polymers107,4636
Non-polymers2,80114
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area22160 Å2
ΔGint-181 kcal/mol
Surface area32100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.630, 121.370, 112.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-358-

HOH

21B-335-

HOH

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Components

#1: Protein Nucleoside diphosphate kinase / Nucleoside-diphosphate kinase / NDK B


Mass: 17910.428 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / Gene: Tb11.01.7800 / Plasmid: pAVA0421 / Production host: Escherichia coli (E. coli) / References: UniProt: Q381H3, nucleoside-diphosphate kinase
#2: Chemical ChemComp-CDP / CYTIDINE-5'-DIPHOSPHATE / Cytidine diphosphate


Mass: 403.176 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H15N3O11P2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 516 / 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: 2.28 Å3/Da / Density % sol: 46.12 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: TrbrA.00438.a.B1 PS01459 at 20.2 mg/mL against 40% MPD, 5% PEG8000, 0.1 M sodium cacodylate, pH 6.5, 2 mM CDP, 10 mM magnesium chloride, crystal tracking ID 234284b5, VAPOR DIFFUSION, ...Details: TrbrA.00438.a.B1 PS01459 at 20.2 mg/mL against 40% MPD, 5% PEG8000, 0.1 M sodium cacodylate, pH 6.5, 2 mM CDP, 10 mM magnesium chloride, crystal tracking ID 234284b5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: May 12, 2012 / Details: VariMax
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 54412 / Num. obs: 53372 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 8.5 % / Biso Wilson estimate: 21.523 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 32.77
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.7-1.740.4383.2414026358390.2
1.74-1.790.4134.319548363593.2
1.79-1.840.3435.2819883359295.1
1.84-1.90.2736.7620271357297.1
1.9-1.960.2258.5220426348498.5
1.96-2.030.18610.6720731341699.6
2.03-2.110.15713.9621338333799.9
2.11-2.190.14118.93248893191100
2.19-2.290.12523.62266993097100
2.29-2.40.11827.06267102929100
2.4-2.530.11830.86273292811100
2.53-2.690.11634283372672100
2.69-2.870.09245.09305652491100
2.87-3.10.07260.48312972352100
3.1-3.40.06673.68289322162100
3.4-3.80.05394.7826160196599.9
3.8-4.390.041113.0422838174099.9
4.39-5.380.042110.3319506149499.9
5.38-7.60.06295.8815255116799.9
7.60.039149.43786368298.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
StructureStudiodata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4F36

4f36


Resolution: 1.7→41.33 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.1552 / WRfactor Rwork: 0.1308 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.9067 / SU B: 3.185 / SU ML: 0.055 / SU R Cruickshank DPI: 0.0933 / SU Rfree: 0.0913 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1821 2628 4.9 %RANDOM
Rwork0.1521 ---
obs0.1536 53338 98.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 45.72 Å2 / Biso mean: 14.9271 Å2 / Biso min: 6.19 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å2-0 Å20 Å2
2--0.06 Å2-0 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.7→41.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3526 0 86 516 4128
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193794
X-RAY DIFFRACTIONr_bond_other_d0.0010.022593
X-RAY DIFFRACTIONr_angle_refined_deg1.5251.9815178
X-RAY DIFFRACTIONr_angle_other_deg0.93636332
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7155487
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.92823.631157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.38715624
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.2631522
X-RAY DIFFRACTIONr_chiral_restr0.090.2567
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214217
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02804
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 140 -
Rwork0.239 3286 -
all-3426 -
obs--89.73 %
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)
10.3862-0.0968-0.02451.1266-0.1160.3736-0.0343-0.0886-0.03140.0782-0.0001-0.09770.05120.05340.03450.01750.01660.00030.0380.01020.019917.399114.439437.3686
20.84580.2604-0.1120.62670.04250.3838-0.02010.099-0.0495-0.1020.0146-0.06850.00110.03840.00560.02850.00570.02270.0433-0.00680.023915.34817.284213.6696
30.68840.21750.0260.52230.08620.3286-0.0051-0.03160.03680.0758-0.0083-0.0185-0.02680.02510.01340.025-0.0033-0.00370.0117-0.00360.00833.504244.451239.8078
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 153
2X-RAY DIFFRACTION1A201 - 202
3X-RAY DIFFRACTION2B2 - 153
4X-RAY DIFFRACTION2B201 - 202
5X-RAY DIFFRACTION3C1 - 153
6X-RAY DIFFRACTION3C201 - 202

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