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- PDB-5trd: Structure of RbkR (Riboflavin Kinase) from Thermoplasma acidophil... -

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Basic information

Entry
Database: PDB / ID: 5trd
TitleStructure of RbkR (Riboflavin Kinase) from Thermoplasma acidophilum determined in complex with CTP and its cognate DNA operator
Components
  • DNA (5'-D(*AP*TP*TP*AP*CP*TP*AP*AP*TP*TP*CP*AP*CP*GP*AP*GP*TP*AP*A)-3')
  • DNA (5'-D(P*TP*TP*TP*AP*CP*TP*CP*GP*TP*GP*AP*AP*TP*TP*AP*GP*TP*AP*A)-3')
  • Riboflavin kinase
KeywordsTRANSFERASE/DNA / ribflavin kinase / MarR type regulatory domain / winged-helix-turn-helix domain / TRANSFERASE-DNA complex
Function / homology
Function and homology information


CTP-dependent riboflavin kinase / riboflavin kinase activity / FMN biosynthetic process / riboflavin biosynthetic process / nucleotide binding / regulation of DNA-templated transcription / DNA binding / metal ion binding
Similarity search - Function
Riboflavin kinase domain, CTP-dependent / Riboflavin kinase, CTP-dependent / Domain of unknown function DUF120 / Riboflavin kinase-like / Riboflavin kinase domain superfamily / Crp-like helix-turn-helix domain / Crp-type HTH domain / Elongation Factor Tu (Ef-tu); domain 3 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A ...Riboflavin kinase domain, CTP-dependent / Riboflavin kinase, CTP-dependent / Domain of unknown function DUF120 / Riboflavin kinase-like / Riboflavin kinase domain superfamily / Crp-like helix-turn-helix domain / Crp-type HTH domain / Elongation Factor Tu (Ef-tu); domain 3 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
CYTIDINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / Riboflavin kinase
Similarity search - Component
Biological speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsVetting, M.W. / Rodionova, I.A. / Li, X. / Osterman, A.L. / Rodionov, D.A. / Almo, S.C.
CitationJournal: To be published
Title: Structure of RbkR (Riboflavin Kinase) from Thermoplasma acidophilum determined in complex with CTP and its cognate DNA operator
Authors: Vetting, M.W. / Rodionova, I.A. / Li, X. / Osterman, A.L. / Rodionov, D.A. / Almo, S.C.
History
DepositionOct 26, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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_prerelease_seq / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Riboflavin kinase
B: Riboflavin kinase
G: DNA (5'-D(*AP*TP*TP*AP*CP*TP*AP*AP*TP*TP*CP*AP*CP*GP*AP*GP*TP*AP*A)-3')
H: DNA (5'-D(P*TP*TP*TP*AP*CP*TP*CP*GP*TP*GP*AP*AP*TP*TP*AP*GP*TP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1488
Polymers64,1364
Non-polymers1,0124
Water7,116395
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7990 Å2
ΔGint-64 kcal/mol
Surface area26150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.411, 95.040, 61.262
Angle α, β, γ (deg.)90.000, 113.510, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Riboflavin kinase / RFK / CTP-dependent riboflavin kinase / CTP:riboflavin 5'-phosphotransferase / Flavokinase


Mass: 26245.066 Da / Num. of mol.: 2 / Fragment: Riboflavin Kinase and Regulator
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic)
Strain: ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165
Gene: ribK, Ta1064 / Plasmid: pET23 derivative / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9HJA6, CTP-dependent riboflavin kinase

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DNA chain , 2 types, 2 molecules GH

#2: DNA chain DNA (5'-D(*AP*TP*TP*AP*CP*TP*AP*AP*TP*TP*CP*AP*CP*GP*AP*GP*TP*AP*A)-3')


Mass: 5811.812 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Thermoplasma acidophilum (acidophilic)
#3: DNA chain DNA (5'-D(P*TP*TP*TP*AP*CP*TP*CP*GP*TP*GP*AP*AP*TP*TP*AP*GP*TP*AP*A)-3')


Mass: 5833.807 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Thermoplasma acidophilum (acidophilic)

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Non-polymers , 3 types, 399 molecules

#4: Chemical ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE


Mass: 483.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16N3O14P3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / 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: 2.43 Å3/Da / Density % sol: 49.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: Crystallization conditions consisted of 0.5 ?L of protein (25 mg ml-1, 1.25 mM ds-DNA, 5 mM CTP) combined with 0.5 ?L of reservoir (0.1M phosphate citrate pH 4.2, 40% ethanol, 5% (w/v) PEG1000)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Dec 6, 2015 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.85→95.04 Å / Num. obs: 50639 / % possible obs: 96.9 % / Redundancy: 3.6 % / Biso Wilson estimate: 24.48 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.037 / Rrim(I) all: 0.071 / Net I/σ(I): 14 / Num. measured all: 182052 / Scaling rejects: 2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.85-1.892.80.6030.687178.9
9.06-95.043.30.0260.998177.9

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Processing

Software
NameVersionClassification
Aimless0.2.8data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CTA

3cta


Resolution: 1.85→49.983 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.85
RfactorNum. reflection% reflection
Rfree0.2165 2578 5.09 %
Rwork0.1742 --
obs0.1764 50605 96.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 132.48 Å2 / Biso mean: 34.0523 Å2 / Biso min: 12.18 Å2
Refinement stepCycle: final / Resolution: 1.85→49.983 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3469 776 60 395 4700
Biso mean--24.89 38.59 -
Num. residues----472
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074474
X-RAY DIFFRACTIONf_angle_d0.9496212
X-RAY DIFFRACTIONf_chiral_restr0.058711
X-RAY DIFFRACTIONf_plane_restr0.005649
X-RAY DIFFRACTIONf_dihedral_angle_d22.8832568
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.88560.3157920.25612195228778
1.8856-1.92410.28261390.24142386252588
1.9241-1.96590.32971360.23592665280197
1.9659-2.01160.24371520.21752687283998
2.0116-2.0620.24481420.20222709285198
2.062-2.11770.24741540.19892689284398
2.1177-2.180.25931380.19132732287099
2.18-2.25040.22811440.18342718286299
2.2504-2.33080.24521640.18942690285499
2.3308-2.42410.24591510.17662732288399
2.4241-2.53450.22351490.17572714286399
2.5345-2.66810.2331440.18572724286899
2.6681-2.83520.23111400.18352735287599
2.8352-3.05410.21681620.18912733289599
3.0541-3.36140.19961520.17212713286599
3.3614-3.84760.21271410.15482767290899
3.8476-4.8470.17641450.13822746289199
4.847-50.0010.16881330.15552692282595
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)
11.6763-1.5155-0.43774.1697-1.15815.97630.03990.35040.124-0.0148-0.0162-0.15150.40890.1656-0.03010.2050.0785-0.0160.17330.00630.15298.8146-9.424922.548
21.1545-0.7830.15081.2352-0.37421.1195-0.0280.0076-0.2120.162-0.0595-0.05440.31250.23070.07830.2640.0548-0.00950.23060.01260.197512.0963-11.532826.94
31.26980.9096-2.15540.6512-1.52463.61410.01910.16110.0424-0.0506-0.04660.11940.1975-0.28530.03660.2174-0.0130.02150.27380.01870.194-10.74140.909628.4276
41.45250.1051-0.88041.4835-0.04282.08830.0326-0.01380.11630.08740.01480.09470.011-0.0099-0.0420.11930.00230.0090.15160.00260.1359-9.1376.916240.6738
52.49841.04220.59942.2211-0.49411.9560.028-0.34370.33480.2527-0.0354-0.0206-0.3276-0.0446-0.0040.2279-0.00260.02470.1834-0.04330.226411.876713.626415.6879
61.06320.0049-0.30440.8485-0.10171.1420.056-0.02060.1469-0.0373-0.0149-0.1044-0.01950.0278-0.03470.14340.0209-0.01260.1627-0.01380.184212.32059.20419.356
71.2557-0.7471.54830.4773-0.90691.88820.157-0.21880.0354-0.1160.01460.20670.2092-0.2658-0.17320.228-0.0131-0.02160.25620.03510.2095-10.5916-0.14428.5722
82.557-0.6872-0.3742.96370.2322.10580.02830.192-0.1773-0.34850.0004-0.34640.2126-0.1507-0.01670.2634-0.0394-0.00860.19320.01130.2902-6.674-14.6591-8.6087
91.5220.6690.57711.89990.12481.5767-0.0515-0.0685-0.0768-0.1260.0206-0.0038-0.0231-0.01140.02950.1635-0.0082-0.00780.14960.01170.1604-5.8199-5.9005-1.189
101.5488-0.15330.01172.5514-0.38511.6609-0.0866-0.29670.1136-0.1744-0.06640.308-0.0389-0.29540.15680.15970.0527-0.04930.2724-0.00670.2422-18.822-3.079-2.3377
116.7349-0.30281.37854.5383-1.30534.63790.3412-0.15440.51660.5773-0.6369-0.1894-0.40740.26040.15040.2569-0.06230.02760.2484-0.0330.465726.497321.117411.5352
123.35310.1310.54362.6613-2.1762.7750.1917-0.6971-0.46390.3015-0.379-0.59190.07950.580.22210.24520.0763-0.11380.71280.25430.903937.41458.210117.0127
131.6125-0.02560.25252.7276-0.57151.9675-0.1464-0.4603-0.56990.0235-0.0331-0.02530.1330.46340.19170.38270.18260.06620.58080.1310.49331.6187-15.178923.6306
144.36291.6745-1.48492.7449-2.11652.55430.106-0.05360.1436-0.4863-0.3615-0.47080.17440.62880.23410.50210.17160.02080.51450.1230.504731.1132-16.088325.0311
151.98230.6758-0.42233.784-0.81172.74720.2194-0.24910.66230.3405-0.5279-0.702-0.01610.82460.2490.3809-0.0216-0.1520.44020.04570.686632.616912.670515.7649
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 21 )A5 - 21
2X-RAY DIFFRACTION2chain 'A' and (resid 22 through 86 )A22 - 86
3X-RAY DIFFRACTION3chain 'A' and (resid 87 through 100 )A87 - 100
4X-RAY DIFFRACTION4chain 'A' and (resid 101 through 223 )A101 - 223
5X-RAY DIFFRACTION5chain 'B' and (resid 7 through 38 )B7 - 38
6X-RAY DIFFRACTION6chain 'B' and (resid 39 through 86 )B39 - 86
7X-RAY DIFFRACTION7chain 'B' and (resid 87 through 100 )B87 - 100
8X-RAY DIFFRACTION8chain 'B' and (resid 101 through 123 )B101 - 123
9X-RAY DIFFRACTION9chain 'B' and (resid 124 through 197 )B124 - 197
10X-RAY DIFFRACTION10chain 'B' and (resid 198 through 221 )B198 - 221
11X-RAY DIFFRACTION11chain 'G' and (resid 1 through 5 )G1 - 5
12X-RAY DIFFRACTION12chain 'G' and (resid 6 through 10 )G6 - 10
13X-RAY DIFFRACTION13chain 'G' and (resid 11 through 19 )G11 - 19
14X-RAY DIFFRACTION14chain 'H' and (resid 1 through 10 )H1 - 10
15X-RAY DIFFRACTION15chain 'H' and (resid 11 through 19 )H11 - 19

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