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- PDB-1eji: RECOMBINANT SERINE HYDROXYMETHYLTRANSFERASE (MOUSE) -

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Basic information

Entry
Database: PDB / ID: 1eji
TitleRECOMBINANT SERINE HYDROXYMETHYLTRANSFERASE (MOUSE)
ComponentsSERINE HYDROXYMETHYLTRANSFERASE
KeywordsTRANSFERASE / SERINE-GLYCINE CONVERSION / PYRIDOXAL 5'-PHOSPHATE / TETRAHYDROFOLATE / ASYMMETRIC DIMER
Function / homology
Function and homology information


Carnitine synthesis / Metabolism of folate and pterines / 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 ...Carnitine synthesis / Metabolism of folate and pterines / 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 / dTMP biosynthetic process / folic acid metabolic process / one-carbon metabolic process / mRNA regulatory element binding translation repressor activity / cellular response to leukemia inhibitory factor / mRNA 5'-UTR binding / pyridoxal phosphate binding / protein homotetramerization / protein homodimerization activity / mitochondrion / nucleoplasm / nucleus / 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
Chem-PLG / 5-HYDROXYMETHYLENE-6-HYDROFOLIC ACID / Serine hydroxymethyltransferase, cytosolic
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsSzebenyi, D.M.E. / Liu, X. / Kriksunov, I.A. / Stover, P.J. / Thiel, D.J.
CitationJournal: Biochemistry / Year: 2000
Title: Structure of a murine cytoplasmic serine hydroxymethyltransferase quinonoid ternary complex: evidence for asymmetric obligate dimers.
Authors: Szebenyi, D.M. / Liu, X. / Kriksunov, I.A. / Stover, P.J. / Thiel, D.J.
History
DepositionMar 2, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_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: SERINE HYDROXYMETHYLTRANSFERASE
B: SERINE HYDROXYMETHYLTRANSFERASE
C: SERINE HYDROXYMETHYLTRANSFERASE
D: SERINE HYDROXYMETHYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,31611
Polymers212,6704
Non-polymers2,6457
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27200 Å2
ΔGint-131 kcal/mol
Surface area65770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.520, 142.520, 270.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

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Components

#1: Protein
SERINE HYDROXYMETHYLTRANSFERASE / SHMT


Mass: 53167.594 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Organ: LIVER / Plasmid: PET28A(+) / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli)
References: UniProt: P50431, glycine hydroxymethyltransferase
#2: Chemical
ChemComp-PLG / N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE] / N-PYRIDOXYL-GLYCINE-5-MONOPHOSPHATE


Mass: 306.209 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N2O7P
#3: Chemical ChemComp-THF / 5-HYDROXYMETHYLENE-6-HYDROFOLIC ACID


Mass: 473.439 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H23N7O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.33 Å3/Da / Density % sol: 62.3 %
Description: RESOLUTION RANGES 3.96-3.84 AND 3.72-3.64 A EXCLUDED FROM PROCESSING BECAUSE OF ICE RINGS.
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.7
Details: 8% PEG 8000, 6% ETHYLENE GLYCOL, 0.1 M HEPES, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18 %PEG80001drop
26 %ethylene glycol1drop
30.1 MHEPES1drop
40.200 mM(6S)-5-formylTHF1drop
5100 mMglycine1drop
64 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.922
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 7, 1999 / Details: MIRROR
RadiationMonochromator: BENT TRIANGULAR SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.922 Å / Relative weight: 1
ReflectionResolution: 2.9→32.1 Å / Num. obs: 57974 / % possible obs: 92.8 % / Observed criterion σ(I): 0 / Redundancy: 10.6 % / Biso Wilson estimate: 78.8 Å2 / Rsym value: 0.203 / Net I/σ(I): 3.4
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 10.9 % / Mean I/σ(I) obs: 0.3 / Rsym value: 2.38 / % possible all: 100
Reflection
*PLUS
Num. measured all: 1046890 / Rmerge(I) obs: 0.203
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.9refinement
DPSdata reduction
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: RABBIT SHMT (1CJ0) DIMER, WITH 2 PLP COFACTORS. EACH MONOMER WAS MODIFIED BY: OMISSION OF RESIDUES 269-287 (IN THE HUMAN SHMT NUMBERING SCHEME; LABELED 241-250 IN THE 1CJ0 ENTRY), ...Starting model: RABBIT SHMT (1CJ0) DIMER, WITH 2 PLP COFACTORS. EACH MONOMER WAS MODIFIED BY: OMISSION OF RESIDUES 269-287 (IN THE HUMAN SHMT NUMBERING SCHEME; LABELED 241-250 IN THE 1CJ0 ENTRY), CONVERSION OF ALL MET RESIDUES TO SEMET, AND CONVERSION TO ALANINE OF RESIDUES WHICH DIFFER BETWEEN RABBIT AND MOUSE, I.E. RESIDUES 16, 20, 35, 68, 88, 94, 175, 177, 182, 185, 191, 220, 237, 322, 326, 329, 332, 343, 361, 416, 433, 437-439, 441-442, 458, 460, 463, 467, 471, 475, AND 477 IN THE HUMAN SHMT NUMBERING SCHEME.

1cj0

1cj0


Resolution: 2.9→32.1 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.228 5780 10.1 %RANDOM
Rwork0.271 ---
obs0.228 57357 91.7 %-
all-62472 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 66.13 Å2 / ksol: 0.347 e/Å3
Displacement parametersBiso mean: 84.6 Å2
Baniso -1Baniso -2Baniso -3
1-12.79 Å20 Å20 Å2
2--12.79 Å20 Å2
3----25.57 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.54 Å0.46 Å
Luzzati d res low-5 Å
Luzzati sigma a0.72 Å0.7 Å
Refinement stepCycle: LAST / Resolution: 2.9→32.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14780 0 182 22 14984
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_improper_angle_d0.9
Refine LS restraints NCS
Ens-IDDom-IDNCS model detailsRefine-IDWeight Biso Weight position
11FOR EACH GROUP, RESTRAINTS WERE APPLIED AMONG THE 4 CHAINS A, B, C, AND D. GROUP 1: MAIN CHAIN ATOMS FOR RESIDUES 15-77, 84-144, 162-256, 259-270, 287-294, 300-382, 400-435, AND 459-479X-RAY DIFFRACTION2400
22GROUP 2: SIDE CHAIN ATOMS FOR RESIDUES 15-74, 84-142, 162-174, 176-202, 204-230, 232-256, 259-270, 287-294, 300-382, 403-435, AND 459-479X-RAY DIFFRACTION2100
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.379 1035 10.1 %
Rwork0.371 9171 -
obs--99.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2PLG2.PARAMPLG2.TOP
X-RAY DIFFRACTION3THF_XPLOR.PARAMTHF_XPLOR.TOP
X-RAY DIFFRACTION4WATER_REP.PARAWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10.1 % / Rfactor Rfree: 0.272
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 84.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.9
LS refinement shell
*PLUS
Rfactor Rfree: 0.379 / % reflection Rfree: 10.1 % / Rfactor Rwork: 0.371

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