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- PDB-1n08: Crystal Structure of Schizosaccharomyces pombe Riboflavin Kinase ... -

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Basic information

Entry
Database: PDB / ID: 1n08
TitleCrystal Structure of Schizosaccharomyces pombe Riboflavin Kinase Reveals a Novel ATP and Riboflavin Binding Fold
Componentsputative riboflavin kinase
KeywordsTRANSFERASE / kinase / phophoryl transferases / flavin cofactors / metal binding
Function / homology
Function and homology information


Vitamin B2 (riboflavin) metabolism / riboflavin metabolic process / riboflavin kinase / riboflavin kinase activity / FMN biosynthetic process / riboflavin biosynthetic process / mitochondrial inner membrane / mitochondrion / zinc ion binding / ATP binding ...Vitamin B2 (riboflavin) metabolism / riboflavin metabolic process / riboflavin kinase / riboflavin kinase activity / FMN biosynthetic process / riboflavin biosynthetic process / mitochondrial inner membrane / mitochondrion / zinc ion binding / ATP binding / nucleus / cytosol
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
ADENOSINE-5'-DIPHOSPHATE / Riboflavin kinase
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsBauer, S. / Kemter, K. / Bacher, A. / Huber, R. / Fischer, M. / Steinbacher, S.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Crystal Structure of Schizosaccharomyces pombe Riboflavin Kinase Reveals a Novel ATP and Riboflavin Binding Fold
Authors: Bauer, S. / Kemter, K. / Bacher, A. / Huber, R. / Fischer, M. / Steinbacher, S.
History
DepositionOct 11, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: 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 / struct_conn / 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_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.ptnr1_label_seq_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_label_seq_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_conn.ptnr2_label_seq_id / _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

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Assembly

Deposited unit
A: putative riboflavin kinase
B: putative riboflavin kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8636
Polymers37,8782
Non-polymers9854
Water4,882271
1
A: putative riboflavin kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4313
Polymers18,9391
Non-polymers4932
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: putative riboflavin kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4313
Polymers18,9391
Non-polymers4932
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.235, 45.321, 52.849
Angle α, β, γ (deg.)89.70, 112.04, 98.41
Int Tables number1
Space group name H-MP1

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Components

#1: Protein putative riboflavin kinase


Mass: 18938.750 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: SPCC18.16C / Plasmid: pNCO / Production host: Escherichia coli (E. coli) / References: UniProt: O74866, riboflavin kinase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / 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: 2.39 Å3/Da / Density % sol: 48.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: PEG 8000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMTris-HCl1droppH8.0
2100 mM1dropNaCl
310 mg/mlprotein1drop
40.1 MMES-NaOH1reservoirpH6.5
50.2 Mmagnesium acetate1reservoir
620 %(w/v)PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.542 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 2, 2002 / Details: mirror
RadiationMonochromator: osmic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. all: 42651 / Num. obs: 42651 / % possible obs: 90.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.044
Reflection shellResolution: 1.6→1.64 Å / Rmerge(I) obs: 0.431 / % possible all: 86.3
Reflection
*PLUS
Lowest resolution: 20 Å / % possible obs: 92.5 % / Redundancy: 3 % / Rmerge(I) obs: 0.043
Reflection shell
*PLUS
% possible obs: 88.5 % / Rmerge(I) obs: 0.404

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N06

1n06


Resolution: 1.6→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2521 2142 -RANDOM
Rwork0.2195 ---
all0.2235 42651 --
obs0.2235 42651 92.2 %-
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2531 0 56 271 2858
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008081
X-RAY DIFFRACTIONc_angle_deg1.31525
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.252 / Rfactor Rwork: 0.219
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3

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