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- PDB-1ls3: Crystal Structure of the Complex between Rabbit Cytosolic Serine ... -

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Basic information

Entry
Database: PDB / ID: 1ls3
TitleCrystal Structure of the Complex between Rabbit Cytosolic Serine Hydroxymethyltransferase and TriGlu-5-formyl-tetrahydrofolate
ComponentsSerine Hydroxymethyltransferase
KeywordsTRANSFERASE / asymmetric tetramer
Function / homology
Function and homology information


cellular response to tetrahydrofolate / purine nucleobase biosynthetic process / serine binding / L-serine catabolic process / glycine metabolic process / L-serine metabolic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate metabolic process ...cellular response to tetrahydrofolate / purine nucleobase biosynthetic process / serine binding / L-serine catabolic process / glycine metabolic process / L-serine metabolic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate metabolic process / tetrahydrofolate interconversion / folic acid metabolic process / mRNA regulatory element binding translation repressor activity / mRNA 5'-UTR binding / pyridoxal phosphate binding / protein homotetramerization / protein homodimerization activity / mitochondrion / nucleoplasm / 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 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (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 1 / Aspartate Aminotransferase, domain 1 / 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 / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GLYCINE / PYRIDOXAL-5'-PHOSPHATE / Chem-TGF / Serine hydroxymethyltransferase, cytosolic
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsFu, T.F. / Scarsdale, J.N. / Kazanina, G. / Schirch, V. / Wright, H.T.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Location of the Pteroylpolyglutamate Binding Site on Rabbit Cytosolic Serine Hydroxymethyltransferase
Authors: Fu, T.F. / Scarsdale, J.N. / Kazanina, G. / Schirch, V. / Wright, H.T.
History
DepositionMay 16, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 21, 2013Group: Non-polymer description
Revision 1.4Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_ins_code / _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: Serine Hydroxymethyltransferase
B: Serine Hydroxymethyltransferase
C: Serine Hydroxymethyltransferase
D: Serine Hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,63516
Polymers211,6644
Non-polymers2,97012
Water6,810378
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26890 Å2
ΔGint-115 kcal/mol
Surface area58770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.084, 114.084, 156.719
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Serine Hydroxymethyltransferase / SERINE METHYLASE / GLYCINE HYDROXYMETHYLTRANSFERASE / SHMT


Mass: 52916.113 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Plasmid: PET 22B(+) / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3)
References: UniProt: p07511, UniProt: P07511*PLUS, glycine hydroxymethyltransferase

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Non-polymers , 5 types, 390 molecules

#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-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO2
#4: Chemical ChemComp-TGF / 2-[4-(4-{4-[(2-AMINO-5-FORMYL-4-OXO-3,4,5,6,7,8-HEXAHYDRO-PTERIDIN-6-YLMETHYL)-AMINO]-BENZOYLAMINO}-4-CARBOXY-BUTYRYLAM INO)-4-CARBOXY-BUTYRYLAMINO]-PENTANEDIOIC ACID / TRIGLU-5-FORMYL-TETRAHYDROFOLATE


Mass: 731.667 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H37N9O13
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / 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: 2.52 Å3/Da / Density % sol: 50.9 %
Crystal growTemperature: 298 K / Method: small tubes / pH: 7
Details: 50 mg/ml Shmt 3% PEG 4000 50 mM Potassium-2(N-morpholino-)ethanesulfonate, pH 7.0, SMALL TUBES, temperature 298K
Crystal grow
*PLUS
Method: unknown / Details: used seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
150 mg/mlprotein11
23 %PEG400011
350 mMpotassium MES11pH7.0

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Dec 7, 2000 / Details: Osmic Confocal optics
RadiationMonochromator: Osmic Confocal Optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→99 Å / Num. all: 55833 / Num. obs: 48527 / Observed criterion σ(I): -3 / Redundancy: 2.2 % / Biso Wilson estimate: 46.1 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 9.9
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.524 / Mean I/σ(I) obs: 1.67 / % possible all: 93.6
Reflection
*PLUS
Num. obs: 48537 / % possible obs: 87 % / Rmerge(I) obs: 0.08
Reflection shell
*PLUS
% possible obs: 94 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 1.7

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2.1 Angstrom Structure of Rabbit Cytosolic Serine Hydroxymethyltransferase

Resolution: 2.7→19.79 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 960476 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.294 4794 10.1 %RANDOM
Rwork0.22 ---
obs0.22 47570 86.7 %-
all-55833 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.9412 Å2 / ksol: 0.267359 e/Å3
Displacement parametersBiso mean: 48.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.65 Å20 Å20 Å2
2---0.65 Å20 Å2
3---1.29 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.36 Å
Luzzati d res low-20 Å
Luzzati sigma a0.51 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.7→19.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13700 0 198 378 14276
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.03
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.405 816 9.6 %
Rwork0.32 7660 -
obs--93.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PLP.PARamWATER.TOP
X-RAY DIFFRACTION3patch_plpur.paramPLP.Top
X-RAY DIFFRACTION4PATCH_PLP2.PARampatch_plpur.top
X-RAY DIFFRACTION5PATCH_PLP_EXTALD.PARamPATCH_PLP2.TOP
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 20 Å / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg2
LS refinement shell
*PLUS
Rfactor Rfree: 0.406 / Rfactor Rwork: 0.321

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