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- PDB-3n0c: TM0449 mutant crystal grown by hanging drop method -

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Basic information

Entry
Database: PDB / ID: 3n0c
TitleTM0449 mutant crystal grown by hanging drop method
ComponentsThymidylate synthase thyX
KeywordsTRANSFERASE / Crystals in loops / thyX / FDTS
Function / homology
Function and homology information


thymidylate synthase (FAD) / thymidylate synthase (FAD) activity / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / NADPH binding / 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
FLAVIN-ADENINE DINUCLEOTIDE / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / Flavin-dependent thymidylate synthase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Rigid body refinemet / Resolution: 2.3 Å
AuthorsMathews, I.I.
Citation
Journal: J.Appl.Crystallogr. / Year: 2010
Title: Diffraction study of protein crystals grown in cryoloops and micromounts.
Authors: Berger, M.A. / Decker, J.H. / Mathews, I.I.
#1: Journal: Structure / Year: 2003
Title: Functional analysis of substrate and cofactor complex structures of a thymidylate synthase-complementing protein.
Authors: Mathews, I.I. / Deacon, A.M. / Canaves, J.M. / McMullan, D. / Lesley, S.A. / Agarwalla, S. / Kuhn, P.
History
DepositionMay 13, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 25, 2012Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Sep 6, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)113,62512
Polymers109,2504
Non-polymers4,3758
Water82946
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23130 Å2
ΔGint-57 kcal/mol
Surface area31800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.549, 116.718, 141.202
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Thymidylate synthase thyX / TS / TSase


Mass: 27312.453 Da / Num. of mol.: 4 / Mutation: F158A,W160A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: thy1, thyX, tm0449, TM_0449 / Plasmid: pMH1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WYT0, thymidylate synthase (FAD)
#2: Chemical
ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP


Mass: 308.182 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H13N2O8P
#3: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.15 Å3/Da / Density % sol: 42.87 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 49% PEG 200, 0.1M HEPES (pH 7.6), VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 25, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. all: 40698 / Num. obs: 40698 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 12.8
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.7 / % possible all: 99.5

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Processing

Software
NameVersionClassification
Blu-Icedata collection
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: Rigid body refinemet
Starting model: PDB ENTRY 3NOB

3nob


Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.913 / SU B: 14.448 / SU ML: 0.169 / Cross valid method: THROUGHOUT / ESU R: 0.42 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24754 2037 5 %RANDOM
Rwork0.19308 ---
obs0.19585 38582 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.197 Å2
Baniso -1Baniso -2Baniso -3
1-2.33 Å20 Å20 Å2
2---0.63 Å20 Å2
3----1.71 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7133 0 292 46 7471
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0227632
X-RAY DIFFRACTIONr_bond_other_d0.0010.025278
X-RAY DIFFRACTIONr_angle_refined_deg1.8322.00210372
X-RAY DIFFRACTIONr_angle_other_deg1.233312727
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6945856
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.33522.403362
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.903151281
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7671568
X-RAY DIFFRACTIONr_chiral_restr0.2160.21121
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0218197
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021691
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_it0.8261.54309
X-RAY DIFFRACTIONr_mcbond_other0.1921.51719
X-RAY DIFFRACTIONr_mcangle_it1.56626976
X-RAY DIFFRACTIONr_scbond_it2.3533323
X-RAY DIFFRACTIONr_scangle_it3.7844.53396
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 147 -
Rwork0.228 2763 -
obs--98.51 %
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)
10.442-0.02730.35910.3530.11792.1232-0.0155-0.02620.0497-0.01210.0272-0.0144-0.1682-0.1992-0.01170.03390.0049-0.00940.02970.00780.014427.946260.473122.2836
20.58550.45110.09521.23060.61820.99670.03210.0096-0.0002-0.16180.0275-0.1647-0.08740.0946-0.05960.0425-0.00610.03540.04960.00680.034144.611745.28997.573
30.39250.0104-0.28550.42750.05231.13480.03810.023-0.0716-0.02040.01690.01020.0903-0.1109-0.0550.0259-0.0188-0.00810.0229-0.0120.063625.385128.1309105.3929
40.2999-0.1868-0.07021.26160.85381.13720.0047-0.0357-0.05040.19250.0829-0.15270.11970.0811-0.08760.03420.0057-0.03410.05040.01110.043940.827740.5679133.6474
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 215
2X-RAY DIFFRACTION2B1 - 220
3X-RAY DIFFRACTION3C1 - 220
4X-RAY DIFFRACTION4D1 - 215

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