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- PDB-6nnr: high-resolution structure of wild-type E. coli thymidylate synthase -

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Basic information

Entry
Database: PDB / ID: 6nnr
Titlehigh-resolution structure of wild-type E. coli thymidylate synthase
ComponentsThymidylate synthase
KeywordsTRANSFERASE / nucleotide synthesis / hydride transfer / methyl transfer / cancer drug target
Function / homology
Function and homology information


thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / response to radiation / regulation of translation / methylation / magnesium ion binding / protein homodimerization activity / RNA binding / cytosol
Similarity search - Function
Thymidylate Synthase; Chain A / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase / Thymidylate synthase, active site / Thymidylate synthase active site. / Thymidylate synthase / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase superfamily / Thymidylate synthase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
10-PROPARGYL-5,8-DIDEAZAFOLIC ACID / 2'-deoxy-5'-uridylic acid / Thymidylate synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.05 Å
AuthorsStroud, R.M. / Finer-Moore, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM42285 United States
Citation
Journal: J. Am. Chem. Soc. / Year: 2013
Title: Mg2+ binds to the surface of thymidylate synthase and affects hydride transfer at the interior active site.
Authors: Wang, Z. / Sapienza, P.J. / Abeysinghe, T. / Luzum, C. / Lee, A.L. / Finer-Moore, J.S. / Stroud, R.M. / Kohen, A.
#1: Journal: J. Am. Chem. Soc. / Year: 2012
Title: A remote mutation affects the hydride transfer by disrupting concerted protein motions in thymidylate synthase.
Authors: Wang, Z. / Abeysinghe, T. / Finer-Moore, J.S. / Stroud, R.M. / Kohen, A.
History
DepositionJan 15, 2019Deposition site: RCSB / Processing site: RCSB
SupersessionJan 30, 2019ID: 4KNZ
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thymidylate synthase
B: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1949
Polymers61,1192
Non-polymers2,0757
Water13,565753
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7030 Å2
ΔGint-19 kcal/mol
Surface area19730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.530, 125.530, 66.757
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Thymidylate synthase / TSase


Mass: 30559.666 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: thyA, b2827, JW2795 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A884, thymidylate synthase

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Non-polymers , 5 types, 760 molecules

#2: Chemical ChemComp-UMC / 2'-deoxy-5'-uridylic acid


Mass: 310.198 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15N2O8P
#3: Chemical ChemComp-CB3 / 10-PROPARGYL-5,8-DIDEAZAFOLIC ACID


Mass: 477.469 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H23N5O6
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 753 / 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: 2.48 Å3/Da / Density % sol: 50.49 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 5.2 mg/ml protein, 17 mM KPO4, 3.3 mM dUMP, 3.3 mM CB3717, 3.3 mM DTT, against 1.44 M Na Citrate

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Data collection

DiffractionMean temperature: 173 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.8855 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 22, 2016
RadiationMonochromator: Double crystal SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8855 Å / Relative weight: 1
ReflectionResolution: 1.05→62.765 Å / Num. obs: 277308 / % possible obs: 99.8 % / Redundancy: 17.84 % / Biso Wilson estimate: 10.3 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 24.22
Reflection shellResolution: 1.05→1.08 Å / Redundancy: 7.15 % / Rmerge(I) obs: 2.55 / Mean I/σ(I) obs: 0.66 / % possible all: 97.2

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Processing

Software
NameVersionClassification
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4KNZ

4knz
PDB Unreleased entry


Resolution: 1.05→62.77 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 13.82
RfactorNum. reflection% reflection
Rfree0.132 2007 0.72 %
Rwork0.121 --
obs0.121 277201 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 15.4 Å2
Refinement stepCycle: LAST / Resolution: 1.05→62.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4297 0 141 753 5191
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014892
X-RAY DIFFRACTIONf_angle_d1.1686681
X-RAY DIFFRACTIONf_dihedral_angle_d20.2511836
X-RAY DIFFRACTIONf_chiral_restr0.083689
X-RAY DIFFRACTIONf_plane_restr0.01874
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.05-1.07630.30321370.328718985X-RAY DIFFRACTION97
1.0763-1.10540.27111410.268919547X-RAY DIFFRACTION100
1.1054-1.13790.20791420.207519663X-RAY DIFFRACTION100
1.1379-1.17460.18241460.166319663X-RAY DIFFRACTION100
1.1746-1.21660.14051420.135419637X-RAY DIFFRACTION100
1.2166-1.26530.14171450.11919605X-RAY DIFFRACTION100
1.2653-1.32290.11141390.10919684X-RAY DIFFRACTION100
1.3229-1.39270.12571460.101619720X-RAY DIFFRACTION100
1.3927-1.47990.13971440.096719696X-RAY DIFFRACTION100
1.4799-1.59420.11131400.08919682X-RAY DIFFRACTION100
1.5942-1.75460.11361480.093719731X-RAY DIFFRACTION100
1.7546-2.00860.1091450.102119741X-RAY DIFFRACTION100
2.0086-2.53060.11561450.112219796X-RAY DIFFRACTION100
2.5306-62.87740.13131470.12120044X-RAY DIFFRACTION100

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