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- PDB-1ci7: TERNARY COMPLEX OF THYMIDYLATE SYNTHASE FROM PNEUMOCYSTIS CARINII -

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Basic information

Entry
Database: PDB / ID: 1ci7
TitleTERNARY COMPLEX OF THYMIDYLATE SYNTHASE FROM PNEUMOCYSTIS CARINII
ComponentsPROTEIN (THYMIDYLATE SYNTHASE)
KeywordsTRANSFERASE / METHYLTRANSFERASE / NUCLEOTIDE BIOSYNTHESIS / HALF-SITES REACTIVITY
Function / homology
Function and homology information


phosphopantothenoylcysteine decarboxylase activity / thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / protein phosphatase inhibitor activity / nuclear periphery / FMN binding / methylation / mitochondrion / cytosol
Similarity search - Function
Thymidylate Synthase; Chain A / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase, active site / Thymidylate synthase active site. / Thymidylate synthase / Thymidylate synthase/dCMP hydroxymethylase / 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'-DEOXYURIDINE 5'-MONOPHOSPHATE / Thymidylate synthase
Similarity search - Component
Biological speciesPneumocystis carinii (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsAnderson, A.C. / O'Neil, R.H. / Delano, W.L. / Stroud, R.M.
CitationJournal: Biochemistry / Year: 1999
Title: The structural mechanism for half-the-sites reactivity in an enzyme, thymidylate synthase, involves a relay of changes between subunits.
Authors: Anderson, A.C. / O'Neil, R.H. / DeLano, W.L. / Stroud, R.M.
History
DepositionApr 8, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Apr 10, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (THYMIDYLATE SYNTHASE)
B: PROTEIN (THYMIDYLATE SYNTHASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,9005
Polymers68,8072
Non-polymers1,0943
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6450 Å2
ΔGint-27 kcal/mol
Surface area23050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.160, 178.760, 54.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121
DetailsTHE ASYMMETRIC UNIT CONSISTS OF ONE DIMER. THE DIMER IS STRUCTURALLY ASYMMETRIC IN THAT BOTH MONOMERS BIND A MOLECULE OF SUBSTRATE, DUMP, BUT ONLY MONOMER A BINDS THE ANTIFOLATE, 10-PROPARGYL-5,8-DIDEAZAFOLATE (CB3717).

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Components

#1: Protein PROTEIN (THYMIDYLATE SYNTHASE) / E.C.2.1.1.45


Mass: 34403.281 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: COVALENT BOND BETWEEN C173 AND DUMP IN MONOMER A / Source: (gene. exp.) Pneumocystis carinii (fungus) / Cellular location: CYTOPLASM / Plasmid: PUETS-1.8 / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): CHI2913 / References: UniProt: P13100, thymidylate synthase
#2: Chemical ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP


Mass: 308.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N2O8P
#3: Chemical ChemComp-CB3 / 10-PROPARGYL-5,8-DIDEAZAFOLIC ACID


Mass: 477.469 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H23N5O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.3 Å3/Da / Density % sol: 42 %
Crystal growpH: 7.4
Details: 100 UM ENZYME, 2 MM DUMP, 2 MM CB3717, 1 MM DTT OVER 14.5 % PEG 8000, 0.25 M ( NH4)2SO4, 5 MM DTT, 0.1 M TRIS, PH 7.4
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12 mMdUMP1drop
22 mMCB37171drop
31 mMdithiothreitol1drop
412.5 %PEG80001reservoir
50.2 Mammonium sulfate1reservoir
6100 mMTris1reservoirpH7.5
71 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 15, 1993 / Details: MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 15344 / % possible obs: 82 % / Redundancy: 3 % / Biso Wilson estimate: 19 Å2 / Rsym value: 12.7 / Net I/σ(I): 5.9
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.06 / Rsym value: 29.9 / % possible all: 69.3
Reflection
*PLUS
Num. obs: 20517 / % possible obs: 81.2 % / Num. measured all: 57081 / Rmerge(I) obs: 0.127

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Processing

Software
NameVersionClassification
X-PLORmodel building
CNS0.4refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: C. NEOFORMANS TS

Resolution: 2.6→50 Å / Rfactor Rfree error: 0.008 / Data cutoff high rms absF: 1926752.48 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.294 1518 9.9 %RANDOM
Rwork0.221 ---
obs0.221 15344 75.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.57 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 23 Å2
Baniso -1Baniso -2Baniso -3
1-4.23 Å20 Å20 Å2
2--7.49 Å20 Å2
3----11.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.63 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4754 0 75 196 5025
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.99
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.11.5
X-RAY DIFFRACTIONc_mcangle_it3.432
X-RAY DIFFRACTIONc_scbond_it2.942
X-RAY DIFFRACTIONc_scangle_it4.422.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.39 200 9.5 %
Rwork0.276 1897 -
obs--63.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PARAM_DUCB.LIGTOPO.DUCB
X-RAY DIFFRACTION3PARAM11.WAT
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 50 Å / σ(F): 2 / % reflection Rfree: 9.9 % / Rfactor obs: 0.216 / Num. reflection obs: 20517
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 22.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.99
X-RAY DIFFRACTIONc_mcbond_it2.11.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Highest resolution: 2.6 Å / Rfactor Rfree: 0.39 / % reflection Rfree: 9.5 % / Rfactor Rwork: 0.276

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