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- PDB-1p4m: CRYSTAL STRUCTURE OF RIBOFLAVIN KINASE -

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Basic information

Entry
Database: PDB / ID: 1p4m
TitleCRYSTAL STRUCTURE OF RIBOFLAVIN KINASE
ComponentsRIBOFLAVIN KINASE
KeywordsTRANSFERASE / BETA BARREL / RIBOFLAVIN KINASE / FLAVIN MONONUCLEOTIDE
Function / homology
Function and homology information


flavin adenine dinucleotide biosynthetic process / Vitamin B2 (riboflavin) metabolism / riboflavin metabolic process / riboflavin kinase / riboflavin kinase activity / FMN biosynthetic process / positive regulation of NAD(P)H oxidase activity / riboflavin biosynthetic process / reactive oxygen species metabolic process / apoptotic process ...flavin adenine dinucleotide biosynthetic process / Vitamin B2 (riboflavin) metabolism / riboflavin metabolic process / riboflavin kinase / riboflavin kinase activity / FMN biosynthetic process / positive regulation of NAD(P)H oxidase activity / riboflavin biosynthetic process / reactive oxygen species metabolic process / apoptotic process / mitochondrion / ATP binding / metal ion binding / cytosol / 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
ADENOSINE-5'-DIPHOSPHATE / FLAVIN MONONUCLEOTIDE / Riboflavin kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKarthikeyan, S. / Zhou, Q. / Mseeh, F. / Grishin, N.V. / Osterman, A.L. / Zhang, H.
CitationJournal: Structure / Year: 2003
Title: Crystal Structure of Human Riboflavin Kinase Reveals a Beta Barrel Fold and a Novel Active Site Arch
Authors: Karthikeyan, S. / Zhou, Q. / Mseeh, F. / Grishin, N.V. / Osterman, A.L. / Zhang, H.
History
DepositionApr 23, 2003Deposition site: RCSB / Processing site: RCSB
SupersessionMay 13, 2003ID: 1NBG
Revision 1.0May 13, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 16, 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 / 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_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_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

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Assembly

Deposited unit
A: RIBOFLAVIN KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6804
Polymers16,7721
Non-polymers9083
Water1,946108
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.097, 57.097, 82.482
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein RIBOFLAVIN KINASE / hypothetical protein FLJ11149


Mass: 16772.084 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FLJ11149 / Plasmid: PPROEX-HTA / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q969G6, riboflavin kinase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.05 Å3/Da / Density % sol: 39.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: NA CACODALYTE, MG ACETATE, PEG 8000 , pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 26, 2002 / Details: OSMIC MIRROR
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 14856 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 28.35 Å2 / Rsym value: 0.053 / Net I/σ(I): 21.4
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.2 / Rsym value: 0.854 / % possible all: 95.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
REFMAC5.1.27refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NB0

1nb0


Resolution: 1.8→28.55 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.597 / SU ML: 0.105 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.144 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.227 719 5.1 %RANDOM
Rwork0.186 ---
obs0.188 13300 94 %-
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: 22.07 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20.33 Å20 Å2
2--0.66 Å20 Å2
3----0.98 Å2
Refinement stepCycle: LAST / Resolution: 1.8→28.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1177 0 59 108 1344
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0211278
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6662.0051735
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7545146
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.1140.2178
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02959
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2190.2530
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.2105
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.246
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.0171.5729
X-RAY DIFFRACTIONr_mcangle_it1.82321177
X-RAY DIFFRACTIONr_scbond_it2.5523549
X-RAY DIFFRACTIONr_scangle_it4.0664.5558
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.376 41
Rwork0.356 814
Refinement TLS params.Method: refined / Origin x: 11.043 Å / Origin y: 31.915 Å / Origin z: 19.664 Å
111213212223313233
T0.0737 Å20.0224 Å2-0.0174 Å2-0.0116 Å2-0.0089 Å2--0.078 Å2
L1.5343 °2-0.8311 °2-0.3442 °2-1.3193 °20.4579 °2--1.4366 °2
S0.0044 Å °-0.0022 Å °0.0022 Å °0.0631 Å °0.0488 Å °-0.0136 Å °0.0679 Å °0.0144 Å °-0.0532 Å °

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