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- PDB-4bf9: Crystal structure of E. coli dihydrouridine synthase C (DusC) (se... -

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Basic information

Entry
Database: PDB / ID: 4bf9
TitleCrystal structure of E. coli dihydrouridine synthase C (DusC) (selenomethionine derivative)
ComponentsTRNA-DIHYDROURIDINE SYNTHASE C
KeywordsOXIDOREDUCTASE / TRNA MODIFICATION
Function / homology
Function and homology information


tRNA-dihydrouridine16 synthase activity / cellular response to redox state / tRNA dihydrouridine synthesis / tRNA dihydrouridine synthase activity / Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor / FMN binding / flavin adenine dinucleotide binding / tRNA binding
Similarity search - Function
Dihydrouridine synthase, C-terminal recognition domain / tRNA-dihydrouridine(16) synthase / tRNA-dihydrouridine(16) synthase, C-terminal / tRNA-dihydrouridine synthase / Bacteriocin As-48; Chain A / tRNA-dihydrouridine synthase, conserved site / DUS-like, FMN-binding domain / Dihydrouridine synthase (Dus) / Uncharacterized protein family UPF0034 signature. / Aldolase class I ...Dihydrouridine synthase, C-terminal recognition domain / tRNA-dihydrouridine(16) synthase / tRNA-dihydrouridine(16) synthase, C-terminal / tRNA-dihydrouridine synthase / Bacteriocin As-48; Chain A / tRNA-dihydrouridine synthase, conserved site / DUS-like, FMN-binding domain / Dihydrouridine synthase (Dus) / Uncharacterized protein family UPF0034 signature. / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / tRNA-dihydrouridine(16) synthase
Similarity search - Component
Biological speciesESCHERICHIA COLI K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
Model type detailsP ATOMS ONLY, CHAIN B
AuthorsByrne, R.T. / Whelan, F. / Konevega, A. / Aziz, N. / Rodnina, M. / Antson, A.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Major Reorientation of tRNA Substrates Defines Specificity of Dihydrouridine Synthases.
Authors: Byrne, R.T. / Jenkins, H.T. / Peters, D.T. / Whelan, F. / Stowell, J. / Aziz, N. / Kasatsky, P. / Rodnina, M.V. / Koonin, E.V. / Konevega, A.L. / Antson, A.A.
History
DepositionMar 16, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2May 13, 2015Group: Database references
Revision 1.3May 27, 2015Group: Database references
Revision 1.4Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_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
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRNA-DIHYDROURIDINE SYNTHASE C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5332
Polymers38,0761
Non-polymers4561
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.140, 94.140, 119.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein TRNA-DIHYDROURIDINE SYNTHASE C / DIHYDROURIDINE SYNTHASE C


Mass: 38076.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI K-12 (bacteria) / Strain: MG1655 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS
References: UniProt: P33371, Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.8 Å3/Da / Density % sol: 68 % / Description: NONE
Crystal growpH: 6.5
Details: MOLECULAR DIMENSIONS MORPHEUS SCREEN CONDITION D3, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9808
DetectorType: ADSC CCD / Detector: CCD / Date: May 6, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9808 Å / Relative weight: 1
ReflectionResolution: 2.6→59.8 Å / Num. obs: 17124 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.7 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 12.2
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.843 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
BUCCANEERmodel building
SCALAdata scaling
SHELXCDphasing
PHASERphasing
PARROTphasing
BUCCANEERphasing
REFMAC5.7.0032refinement
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.6→58.17 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.94 / SU B: 15.027 / SU ML: 0.16 / Cross valid method: THROUGHOUT / ESU R: 0.318 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.21447 860 5 %RANDOM
Rwork0.17668 ---
obs0.17858 16226 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 53.164 Å2
Baniso -1Baniso -2Baniso -3
1-0.91 Å20 Å20 Å2
2--0.91 Å20 Å2
3----1.82 Å2
Refinement stepCycle: LAST / Resolution: 2.6→58.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2495 0 31 104 2630
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192577
X-RAY DIFFRACTIONr_bond_other_d0.0010.022500
X-RAY DIFFRACTIONr_angle_refined_deg1.4311.9833505
X-RAY DIFFRACTIONr_angle_other_deg0.77735730
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2745317
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.19424.103117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.52115421
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8321521
X-RAY DIFFRACTIONr_chiral_restr0.0710.2391
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213013
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02580
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4562.9571271
X-RAY DIFFRACTIONr_mcbond_other1.4562.9561270
X-RAY DIFFRACTIONr_mcangle_it2.3084.4311587
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.8833.161306
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0674.6581919
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 59 -
Rwork0.28 1175 -
obs--99.92 %
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)
13.01120.4093-1.4273.0643-0.51161.86820.05320.19030.1192-0.1864-0.00540.1972-0.1228-0.1865-0.04780.040.0128-0.03270.02280.00450.049114.386231.148350.6883
23.28490.72571.0158.3275-4.02388.7067-0.03110.27740.8186-0.08440.26430.6487-1.5297-0.7064-0.23330.48090.13930.14280.18660.0180.38863.050252.634460.7238
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 228
2X-RAY DIFFRACTION2A229 - 315

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