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- PDB-4p5a: Crystal structure of a UMP/dUMP methylase PolB from Streptomyces ... -

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Basic information

Entry
Database: PDB / ID: 4p5a
TitleCrystal structure of a UMP/dUMP methylase PolB from Streptomyces cacaoi bound with 5-Br UMP
ComponentsThymidylate synthase ThyX
KeywordsTRANSFERASE / Tetramer / UMP/dUMP methylase / ThyX homolog
Function / homology
Function and homology information


thymidylate synthase (FAD) / thymidylate synthase (FAD) activity / dTMP biosynthetic process / dTTP biosynthetic process / flavin adenine dinucleotide binding / methylation
Similarity search - Function
Gyrase A; domain 2 - #170 / Thymidylate synthase ThyX / Thymidylate synthase ThyX superfamily / Thymidylate synthase complementing protein / Flavin-dependent thymidylate synthase (thyX) domain profile. / Gyrase A; domain 2 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
5-BROMO-URIDINE-5'-MONOPHOSPHATE / FLAVIN-ADENINE DINUCLEOTIDE / Flavin-dependent thymidylate synthase
Similarity search - Component
Biological speciesStreptomyces cacaoi subsp. asoensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.76 Å
AuthorsLi, Y. / Chen, W. / Li, J. / Xia, Z. / Deng, Z. / Zhou, J.
CitationJournal: To Be Published
Title: Crystal structure of a UMP/dUMP methylase PolB from Streptomyces cacaoi with 5-Br UMP
Authors: Li, Y. / Chen, W. / Li, J. / Xia, Z. / Deng, Z. / Zhou, J.
History
DepositionMar 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thymidylate synthase ThyX
B: Thymidylate synthase ThyX
C: Thymidylate synthase ThyX
D: Thymidylate synthase ThyX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,26112
Polymers108,5064
Non-polymers4,7558
Water13,205733
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26120 Å2
ΔGint-42 kcal/mol
Surface area31020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.897, 94.160, 91.948
Angle α, β, γ (deg.)90.00, 98.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Thymidylate synthase ThyX / TSase


Mass: 27126.588 Da / Num. of mol.: 4 / Fragment: UNP residues 19-257
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces cacaoi subsp. asoensis (bacteria)
Gene: polB, thyX / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: C1IC19, thymidylate synthase (FAD)
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-5BU / 5-BROMO-URIDINE-5'-MONOPHOSPHATE


Type: RNA linking / Mass: 403.077 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H12BrN2O9P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 733 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M HEPES, pH 7.5, 10%PEG4000, 5 % isopropanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9798 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 9, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. obs: 103864 / % possible obs: 98.7 % / Redundancy: 7.5 % / Net I/σ(I): 13.49

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Processing

SoftwareName: REFMAC / Version: 5.5.0102 / Classification: refinement
RefinementResolution: 1.76→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.784 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19251 5222 5 %RANDOM
Rwork0.15378 ---
obs0.15572 98597 98.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.28 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20 Å20.5 Å2
2---0.33 Å20 Å2
3----0.15 Å2
Refinement stepCycle: 1 / Resolution: 1.76→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7218 0 300 733 8251
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0227764
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2851.99510582
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8665909
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.71120.845367
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.733151226
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.56515107
X-RAY DIFFRACTIONr_chiral_restr0.4230.21163
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0215933
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.6171.54531
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.71127316
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.99133233
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.1634.53261
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: 1.757→1.803 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 358 -
Rwork0.207 6948 -
obs--93.46 %

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