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- PDB-4f4a: Crystal structure of Nucleoside diphosphate kinase B from Trypano... -

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Basic information

Entry
Database: PDB / ID: 4f4a
TitleCrystal structure of Nucleoside diphosphate kinase B from Trypanosoma brucei, UDP-bound form
ComponentsNucleoside diphosphate kinaseNucleoside-diphosphate kinase
KeywordsTRANSFERASE / SSGCID / NIH / NIAID / SBRI / Emerald BioStructures / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


nucleoside-diphosphate kinase / ciliary plasm / CTP biosynthetic process / UTP 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
URIDINE-5'-DIPHOSPHATE / Nucleoside diphosphate kinase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of Nucleoside diphosphate kinase B from Trypanosoma brucei, UDP-bound form
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Gardberg, A.S. / Edwards, T.E. / Staker, B. / Stewart, L.
History
DepositionMay 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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_comp_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.ptnr1_label_comp_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_comp_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.ptnr3_label_comp_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)52,8189
Polymers51,5333
Non-polymers1,2856
Water7,494416
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)105,63618
Polymers103,0656
Non-polymers2,57112
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area21180 Å2
ΔGint-164 kcal/mol
Surface area32370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.830, 121.510, 113.170
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-394-

HOH

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Components

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


Mass: 17177.566 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: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q381H3, nucleoside-diphosphate kinase
#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 416 / 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: 2.4 Å3/Da / Density % sol: 48.66 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7
Details: EBS internal tracking number 234285A5: JCSG A5, protein: 20.2 mg/mL TrbrA.00438.a.B1 PS01459 in 25 mM HEPES, pH 7.0, 500 mM sodium chloride, 2 mM DTT, 0.025% sodium azide, 5% glycerol, ...Details: EBS internal tracking number 234285A5: JCSG A5, protein: 20.2 mg/mL TrbrA.00438.a.B1 PS01459 in 25 mM HEPES, pH 7.0, 500 mM sodium chloride, 2 mM DTT, 0.025% sodium azide, 5% glycerol, crystallant: 20% PEG3350, 200 mM magnesium formate, 2 mM UDP, 10 mM magnesium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: May 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.1→41.744 Å / Num. obs: 28728 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 22.959 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 23.16
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.1-2.150.2577.511208197491.9
2.15-2.210.2479.514368202797.4
2.21-2.280.24110.313452196497.3
2.28-2.350.20511.214212193697.9
2.35-2.420.17812.113811187998
2.42-2.510.15913.413340181598.4
2.51-2.60.14713.912965175898.4
2.6-2.710.14314.712275170198.7
2.71-2.830.11416.612176165298.9
2.83-2.970.0919.911507156099
2.97-3.130.06924.210938148699.2
3.13-3.320.05628.810552142999.2
3.32-3.550.04738.59657134299.3
3.55-3.830.04244.28929124299
3.83-4.20.03453.48234116899.4
4.2-4.70.03153.87676105499.4
4.7-5.420.03745.5679994199.7
5.42-6.640.04437.4573380099.6
6.64-9.390.03250.3442563399.4
9.390.0274.3234736796.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å41.78 Å
Translation2.5 Å41.78 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.004data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→41.744 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.924 / SU B: 6.428 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.202 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.195 1444 5 %RANDOM
Rwork0.158 ---
obs0.16 28728 98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.846 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å2-0 Å2-0 Å2
2--0.12 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 2.1→41.744 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3499 0 78 416 3993
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193666
X-RAY DIFFRACTIONr_bond_other_d0.0060.022504
X-RAY DIFFRACTIONr_angle_refined_deg1.461.9794976
X-RAY DIFFRACTIONr_angle_other_deg1.14636096
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8085453
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.26423.725153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.97215602
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.2711521
X-RAY DIFFRACTIONr_chiral_restr0.0840.2541
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214031
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02762
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 101 -
Rwork0.167 1784 -
all-1885 -
obs--91.5 %
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)
10.6235-0.0804-0.04121.0742-0.12960.4986-0.059-0.1008-0.05170.07290.0381-0.05840.01120.09020.02090.01160.01810.00120.05180.00920.023517.371114.030337.4601
21.16540.1881-0.01040.4613-0.15220.6527-0.01340.1689-0.0364-0.0728-0.003-0.03330.00690.11910.01640.0290.00020.02360.0753-0.01390.029515.439417.477613.6591
30.78410.27420.1260.67150.13970.3702-0.0081-0.04120.03440.06240.0072-0.0175-0.13440.0130.00090.0858-0.0089-0.00410.0072-0.00750.01653.605344.397439.9069
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 151
2X-RAY DIFFRACTION1A201 - 202
3X-RAY DIFFRACTION2B2 - 151
4X-RAY DIFFRACTION2B201 - 202
5X-RAY DIFFRACTION3C1 - 152
6X-RAY DIFFRACTION3C201 - 202

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