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- PDB-3bnw: Crystal structure of riboflavin kinase from Trypanosoma brucei -

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Basic information

Entry
Database: PDB / ID: 3bnw
TitleCrystal structure of riboflavin kinase from Trypanosoma brucei
ComponentsRiboflavin kinase, putative
KeywordsTRANSFERASE / apo structure / Structural Genomics / Structural Genomics of Pathogenic Protozoa Consortium / SGPP / Kinase / PSI-2 / Protein Structure Initiative
Function / homology
Function and homology information


riboflavin metabolic process / riboflavin kinase / riboflavin kinase activity / FMN biosynthetic process / riboflavin biosynthetic process / nuclear lumen / ATP binding / cytoplasm
Similarity search - Function
Riboflavin kinase domain, bacterial/eukaryotic / Riboflavin kinase / Riboflavin kinase / Riboflavin kinase / Riboflavin kinase-like / Riboflavin kinase domain superfamily / Elongation Factor Tu (Ef-tu); domain 3 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMerritt, E.A. / Holmes, M. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP)
CitationJournal: To be Published
Title: Riboflavin kinase from Trypanosoma brucei.
Authors: Merritt, E.A. / Holmes, M.
History
DepositionDec 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Riboflavin kinase, putative
B: Riboflavin kinase, putative


Theoretical massNumber of molelcules
Total (without water)41,2492
Polymers41,2492
Non-polymers00
Water81145
1
A: Riboflavin kinase, putative


Theoretical massNumber of molelcules
Total (without water)20,6241
Polymers20,6241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Riboflavin kinase, putative


Theoretical massNumber of molelcules
Total (without water)20,6241
Polymers20,6241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
A: Riboflavin kinase, putative

B: Riboflavin kinase, putative


Theoretical massNumber of molelcules
Total (without water)41,2492
Polymers41,2492
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area2880 Å2
ΔGint-19 kcal/mol
Surface area15430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.695, 65.604, 62.690
Angle α, β, γ (deg.)90.00, 103.49, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Riboflavin kinase, putative


Mass: 20624.361 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Strain: 927/4 GUTat10.1 / Gene: Tb09.211.3420 / Plasmid: pET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PlysS / References: UniProt: Q38DG4, riboflavin kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 1.92 Å3/Da / Density % sol: 36.08 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 20% PEG 3350, 0.28M KF, 0.1M HEPES, 5mM DTT, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97915 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 22, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.4→38.6 Å / Num. all: 10719 / Num. obs: 10719 / % possible obs: 88 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 52 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 10.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
Blu-Icedata collection
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Hybrid model generated by Rosetta

Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.89 / SU B: 29.819 / SU ML: 0.326 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 6.294 / ESU R Free: 0.369 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. FROM TLS REFINEMENT, ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.28857 510 4.8 %RANDOM
Rwork0.2128 ---
obs0.21616 10179 86.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.677 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å20 Å20.01 Å2
2--1.11 Å20 Å2
3----0.63 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2494 0 0 45 2539
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222568
X-RAY DIFFRACTIONr_bond_other_d0.0010.021738
X-RAY DIFFRACTIONr_angle_refined_deg0.9611.9523482
X-RAY DIFFRACTIONr_angle_other_deg0.76534230
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6225311
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.0724115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.97815398
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.42158
X-RAY DIFFRACTIONr_chiral_restr0.0550.2373
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022841
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02547
X-RAY DIFFRACTIONr_nbd_refined0.1720.2473
X-RAY DIFFRACTIONr_nbd_other0.1720.21713
X-RAY DIFFRACTIONr_nbtor_refined0.1810.21236
X-RAY DIFFRACTIONr_nbtor_other0.0820.21304
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.265
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1070.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1660.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1620.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.42221681
X-RAY DIFFRACTIONr_mcbond_other0.0562636
X-RAY DIFFRACTIONr_mcangle_it0.71932539
X-RAY DIFFRACTIONr_scbond_it0.71341101
X-RAY DIFFRACTIONr_scangle_it1.0176943
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.589 22 -
Rwork0.355 400 -
obs--47.15 %
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)
15.2603-0.6-1.41631.7594-0.48174.54450.17010.70670.0249-0.1185-0.0869-0.1091-0.0681-0.1477-0.08310.0850.0290.04760.6466-0.01020.04517.39748.10629.129
23.42370.31470.78471.77650.41657.76030.1248-0.4041-0.08690.09060.02550.1407-0.0239-0.8134-0.15020.05420.04620.06620.61590.04790.065-9.86144.98654.313
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 1718 - 179
2X-RAY DIFFRACTION2BB5 - 17113 - 179

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