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- PDB-1bj4: RECOMBINANT SERINE HYDROXYMETHYLTRANSFERASE (HUMAN) -

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Basic information

Entry
Database: PDB / ID: 1bj4
TitleRECOMBINANT SERINE HYDROXYMETHYLTRANSFERASE (HUMAN)
ComponentsSerine hydroxymethyltransferase, cytosolic
KeywordsTRANSFERASE / METABOLIC ROLE / PYRIDOXAL 5'-PHOSPHATE
Function / homology
Function and homology information


cellular response to tetrahydrofolate / Carnitine synthesis / purine nucleobase biosynthetic process / serine binding / L-serine catabolic process / L-serine metabolic process / glycine metabolic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine ...cellular response to tetrahydrofolate / Carnitine synthesis / purine nucleobase biosynthetic process / serine binding / L-serine catabolic process / L-serine metabolic process / glycine metabolic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / Metabolism of folate and pterines / tetrahydrofolate metabolic process / tetrahydrofolate interconversion / dTMP biosynthetic process / folic acid metabolic process / small molecule binding / cellular response to leukemia inhibitory factor / mRNA regulatory element binding translation repressor activity / mRNA 5'-UTR binding / pyridoxal phosphate binding / protein homotetramerization / negative regulation of translation / protein homodimerization activity / extracellular exosome / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
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) / Pyridoxal phosphate-dependent transferase, small 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
PYRIDOXAL-5'-PHOSPHATE / Serine hydroxymethyltransferase, cytosolic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.65 Å
AuthorsRenwick, S.B. / Snell, K.
CitationJournal: Structure / Year: 1998
Title: The crystal structure of human cytosolic serine hydroxymethyltransferase: a target for cancer chemotherapy
Authors: Renwick, S.B. / Snell, K. / Baumann, U.
History
DepositionJul 2, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Aug 16, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 2.0Feb 8, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / database_2 ...atom_site / database_2 / diffrn_source / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_distant_solvent_atoms / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_xplor_file / refine / refine_hist / refine_ls_shell / reflns / reflns_shell / software / struct_conf / struct_conn / struct_ref / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_comp_id / _atom_site.label_comp_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _entity.formula_weight / _entity.pdbx_description / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly_seq.mon_id / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _refine.aniso_B[1][1] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[2][3] / _refine.aniso_B[3][3] / _refine.pdbx_data_cutoff_high_absF / _refine.pdbx_data_cutoff_low_absF / _refine.pdbx_ls_sigma_F / _refine_hist.cycle_id / _refine_ls_shell.percent_reflns_obs / _reflns.percent_possible_obs / _reflns_shell.percent_possible_all / _software.classification / _software.name / _software.version / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_class / _struct_conf.pdbx_PDB_helix_id / _struct_conf.pdbx_PDB_helix_length / _struct_conn.pdbx_leaving_atom_flag / _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_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 / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine hydroxymethyltransferase, cytosolic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9712
Polymers51,7241
Non-polymers2471
Water1,74797
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)154.400, 154.400, 235.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

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


Mass: 51723.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: BREAST / Gene: SHMT1 / Plasmid: PET-14B / Cellular location (production host): CYTOPLASM / Gene (production host): GLYC_HUMAN / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS
References: UniProt: P34896, glycine hydroxymethyltransferase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2

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Sample preparation

CrystalDensity Matthews: 7.5 Å3/Da / Density % sol: 85 %
Crystal growpH: 6.5 / Details: 2 M SODIUM ACETATE, PH 6.5
Crystal grow
*PLUS
Temperature: 286 K / Method: vapor diffusion, hanging drop / Details: Renwick, S.B., (1998) Acta Cryst., D54, 1030.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
122-27 mg/mlprotein1drop
21.0 Msodium acetate1reservoir
30.1 Mimidazole1reservoir

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9995
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 15, 1997 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9995 Å / Relative weight: 1
ReflectionResolution: 2.65→40 Å / Num. obs: 49366 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 10.1 % / Biso Wilson estimate: 60.9 Å2 / Rmerge(I) obs: 0.102 / Rsym value: 0.102 / Net I/σ(I): 22.2
Reflection shellResolution: 2.65→2.68 Å / Redundancy: 10 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.491 / % possible all: 96.6
Reflection
*PLUS
Num. measured all: 500988
Reflection shell
*PLUS
% possible obs: 25.9 % / Rmerge(I) obs: 0.659

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Processing

Software
NameVersionClassification
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
MLPHAREphasing
CCP4model building
CCP4phasing
RefinementMethod to determine structure: MIR / Resolution: 2.65→40 Å / Rfactor Rfree error: 0.015 / Data cutoff high absF: 100000000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.226 2760 5.5 %RANDOM
Rwork0.21 ---
obs0.21 48595 96.6 %-
Displacement parametersBiso mean: 61.1 Å2
Baniso -1Baniso -2Baniso -3
1--5 Å21.5 Å20 Å2
2---5 Å20 Å2
3---30 Å2
Refinement stepCycle: 1 / Resolution: 2.65→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3616 0 15 97 3728
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.1
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.661.5
X-RAY DIFFRACTIONx_mcangle_it4.22
X-RAY DIFFRACTIONx_scbond_it4.42
X-RAY DIFFRACTIONx_scangle_it62.5
LS refinement shellResolution: 2.65→2.68 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.468 48 5.6 %
Rwork0.4472 1207 -
obs--96 %
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 40 Å / σ(F): 0 / % reflection Rfree: 5.5 % / Rfactor obs: 0.21 / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 61.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.1
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it4.42
X-RAY DIFFRACTIONx_mcangle_it4.22
X-RAY DIFFRACTIONx_scangle_it62.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.468 / % reflection Rfree: 5.6 %

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