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- PDB-6fl5: Structure of human SHMT1-H135N-R137A-E168N mutant at 3.6 Ang. res... -

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Basic information

Entry
Database: PDB / ID: 6fl5
TitleStructure of human SHMT1-H135N-R137A-E168N mutant at 3.6 Ang. resolution
ComponentsSerine hydroxymethyltransferase, cytosolic
KeywordsTRANSFERASE / serine hydroxymethyltransferase / Interface / Tetramer / OCM / serine / THF / glicine / TCA
Function / homology
Function and homology information


cellular response to tetrahydrofolate / Carnitine synthesis / carnitine biosynthetic process / purine nucleobase biosynthetic process / serine binding / L-serine catabolic process / glycine metabolic process / L-serine metabolic process / aldehyde-lyase activity / glycine hydroxymethyltransferase ...cellular response to tetrahydrofolate / Carnitine synthesis / carnitine biosynthetic process / purine nucleobase biosynthetic process / serine binding / L-serine catabolic process / glycine metabolic process / L-serine metabolic process / aldehyde-lyase activity / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / Metabolism of folate and pterines / tetrahydrofolate metabolic process / tetrahydrofolate interconversion / dTMP biosynthetic process / small molecule binding / folic acid metabolic process / mRNA regulatory element binding translation repressor activity / cellular response to leukemia inhibitory factor / mRNA 5'-UTR binding / pyridoxal phosphate binding / protein homotetramerization / negative regulation of translation / protein homodimerization activity / mitochondrion / extracellular exosome / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Serine hydroxymethyltransferase, pyridoxal phosphate binding site / Serine hydroxymethyltransferase pyridoxal-phosphate attachment site. / : / Serine hydroxymethyltransferase / Serine hydroxymethyltransferase-like domain / Serine hydroxymethyltransferase / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain ...Serine hydroxymethyltransferase, pyridoxal phosphate binding site / Serine hydroxymethyltransferase pyridoxal-phosphate attachment site. / : / Serine hydroxymethyltransferase / Serine hydroxymethyltransferase-like domain / Serine hydroxymethyltransferase / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Serine hydroxymethyltransferase, cytosolic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.6 Å
AuthorsGiardina, G. / Cutruzzola, F. / Lucchi, R.
Funding support Italy, 4items
OrganizationGrant numberCountry
Associazione Italiana Ricerca sul CancroAIRC-IG2015 n. 16720 to FC Italy
Regione LazioFILAS-RU- 2014-1020 Italy
Fondazione Italiana Ricerca sul CancroTriennal FIRC Fellowship Rif. 14843 Italy
Sapienza - University of RomeC26A149EC4 Italy
CitationJournal: FEBS J. / Year: 2018
Title: The catalytic activity of serine hydroxymethyltransferase is essential for de novo nuclear dTMP synthesis in lung cancer cells.
Authors: Giardina, G. / Paone, A. / Tramonti, A. / Lucchi, R. / Marani, M. / Magnifico, M.C. / Bouzidi, A. / Pontecorvi, V. / Guiducci, G. / Zamparelli, C. / Rinaldo, S. / Paiardini, A. / ...Authors: Giardina, G. / Paone, A. / Tramonti, A. / Lucchi, R. / Marani, M. / Magnifico, M.C. / Bouzidi, A. / Pontecorvi, V. / Guiducci, G. / Zamparelli, C. / Rinaldo, S. / Paiardini, A. / Contestabile, R. / Cutruzzola, F.
History
DepositionJan 25, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine hydroxymethyltransferase, cytosolic
D: Serine hydroxymethyltransferase, cytosolic
G: Serine hydroxymethyltransferase, cytosolic
J: Serine hydroxymethyltransferase, cytosolic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,91412
Polymers206,7834
Non-polymers1,1308
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)139.719, 139.719, 267.377
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12A
22G
13A
23J
14D
24G
15D
25J
16G
26J

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPGLYGLYAA11 - 4791 - 469
21ASPASPGLYGLYDB11 - 4791 - 469
12ASPASPLEULEUAA11 - 4801 - 470
22ASPASPLEULEUGC11 - 4801 - 470
13SERSERLEULEUAA16 - 4806 - 470
23SERSERLEULEUJD16 - 4806 - 470
14ASPASPLEULEUDB11 - 4801 - 470
24ASPASPLEULEUGC11 - 4801 - 470
15SERSERLEULEUDB16 - 4806 - 470
25SERSERLEULEUJD16 - 4806 - 470
16SERSERGLYGLYGC16 - 4796 - 469
26SERSERGLYGLYJD16 - 4796 - 469

NCS ensembles :
ID
1
2
3
4
5
6

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.735789, 0.677211, 0.000372), (0.677206, 0.735782, 0.004096), (0.0025, 0.003266, -0.999992)48.106812, -18.83696, 44.940491
3given(1), (1), (1)
4given(-0.84212, -0.037923, -0.537955), (-0.078302, -0.978356, 0.191544), (-0.533575, 0.203426, 0.820923)0.63884, -169.508179, 18.8668
5given(1), (1), (1)
6given(0.576164, -0.619238, 0.533459), (-0.606374, -0.761487, -0.229016), (0.548037, -0.191525, -0.814232)-65.089684, -144.370071, 27.79842
7given(1), (1), (1)
8given(0.565262, -0.634138, 0.527587), (-0.629651, -0.744873, -0.220692), (0.532935, -0.207447, -0.820333)-67.1744, -143.091995, 25.438511
9given(1), (1), (1)
10given(-0.833203, -0.060538, -0.549644), (-0.054184, -0.980267, 0.190104), (-0.550307, 0.188178, 0.813481)-1.76627, -169.078842, 16.585991
11given(1), (1), (1)
12given(-0.730138, 0.683293, 0.00314), (0.682885, 0.729527, 0.038192), (0.023806, 0.03003, -0.999265)48.617661, -20.28437, 47.505409

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Components

#1: Protein
Serine hydroxymethyltransferase, cytosolic / SHMT / Glycine hydroxymethyltransferase / Serine methylase


Mass: 51695.797 Da / Num. of mol.: 4 / Mutation: H135N, R137A, E168N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SHMT1 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P34896, glycine hydroxymethyltransferase
#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl

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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: 3.17 Å3/Da / Density % sol: 61.24 % / Description: rod like crystals
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2 microL of 80microM protein solution in: 20 mM Hepes pH7.2, 250 mM NaCl 5% glycerol + 2 microL of reservoir:0.1 M Na Cacodilate pH6.5 - 1M Na citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Mar 10, 2017 / Details: CRL
RadiationMonochromator: C(110) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 3.6→56.61 Å / Num. obs: 30938 / % possible obs: 98.2 % / Redundancy: 6.3 % / CC1/2: 0.973 / Rmerge(I) obs: 0.312 / Rpim(I) all: 0.131 / Rrim(I) all: 0.34 / Net I/σ(I): 5.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
3.6-3.796.51.01944710.570.4251.10799.2
11.38-56.615.60.07511390.9960.0330.08298.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.57
Highest resolutionLowest resolution
Rotation123.83 Å3.65 Å

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
XDSdata reduction
Aimless0.5.32data scaling
MOLREPphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BJ4

1bj4


Resolution: 3.6→50.01 Å / Cor.coef. Fo:Fc: 0.865 / Cor.coef. Fo:Fc free: 0.83 / SU B: 44.648 / SU ML: 0.62 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.716
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2771 1545 5 %RANDOM
Rwork0.2622 ---
obs0.263 29318 98.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 160.73 Å2 / Biso mean: 74.364 Å2 / Biso min: 19.04 Å2
Baniso -1Baniso -2Baniso -3
1-2.93 Å20 Å20 Å2
2--2.93 Å20 Å2
3----5.85 Å2
Refinement stepCycle: final / Resolution: 3.6→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14328 0 64 0 14392
Biso mean--64.37 --
Num. residues----1866
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01914677
X-RAY DIFFRACTIONr_bond_other_d00.0213592
X-RAY DIFFRACTIONr_angle_refined_deg0.6381.97119862
X-RAY DIFFRACTIONr_angle_other_deg0.508331547
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.55351860
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.06824.1639
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.18152477
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6581587
X-RAY DIFFRACTIONr_chiral_restr0.0350.22207
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.02116430
X-RAY DIFFRACTIONr_gen_planes_other00.022913
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION / Type: TIGHT THERMAL / Weight position: 0.87

Ens-IDAuth asym-IDNumberRms dev position (Å)
1A35954.14
2A35906.03
3A351812.96
4D35886.11
5D351612.66
6G351011.32
LS refinement shellResolution: 3.6→3.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 114 -
Rwork0.364 2151 -
all-2265 -
obs--99.43 %

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