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- PDB-1dfo: CRYSTAL STRUCTURE AT 2.4 ANGSTROM RESOLUTION OF E. COLI SERINE HY... -

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Basic information

Entry
Database: PDB / ID: 1dfo
TitleCRYSTAL STRUCTURE AT 2.4 ANGSTROM RESOLUTION OF E. COLI SERINE HYDROXYMETHYLTRANSFERASE IN COMPLEX WITH GLYCINE AND 5-FORMYL TETRAHYDROFOLATE
ComponentsSERINE HYDROXYMETHYLTRANSFERASE
KeywordsTRANSFERASE / ALPHA PLP ASPARTATE / AMINO TRANSFERASE / (AAT)-LIKE FOLD
Function / homology
Function and homology information


glycine catabolic process / L-allo-threonine aldolase activity / L-serine biosynthetic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / serine binding / L-serine catabolic process / tetrahydrofolate metabolic process / tetrahydrofolate interconversion ...glycine catabolic process / L-allo-threonine aldolase activity / L-serine biosynthetic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / serine binding / L-serine catabolic process / tetrahydrofolate metabolic process / tetrahydrofolate interconversion / cobalt ion binding / folic acid metabolic process / pyridoxal phosphate binding / protein homodimerization activity / zinc ion binding / identical protein binding / membrane / 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 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
Chem-FFO / Chem-PLG / Serine hydroxymethyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsScarsdale, J.N. / Radaev, S. / Kazanina, G. / Schirch, V. / Wright, H.T.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Crystal structure at 2.4 A resolution of E. coli serine hydroxymethyltransferase in complex with glycine substrate and 5-formyl tetrahydrofolate.
Authors: Scarsdale, J.N. / Radaev, S. / Kazanina, G. / Schirch, V. / Wright, H.T.
History
DepositionNov 20, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)184,60912
Polymers181,4904
Non-polymers3,1198
Water6,990388
1
A: SERINE HYDROXYMETHYLTRANSFERASE
B: SERINE HYDROXYMETHYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,3046
Polymers90,7452
Non-polymers1,5594
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10940 Å2
ΔGint-56 kcal/mol
Surface area25990 Å2
MethodPISA
2
C: SERINE HYDROXYMETHYLTRANSFERASE
D: SERINE HYDROXYMETHYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,3046
Polymers90,7452
Non-polymers1,5594
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10780 Å2
ΔGint-57 kcal/mol
Surface area26030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.460, 172.240, 95.050
Angle α, β, γ (deg.)90.00, 104.12, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
SERINE HYDROXYMETHYLTRANSFERASE / SHMT / SERINE METHYLASE


Mass: 45372.477 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PBR322 / Production host: Escherichia coli (E. coli)
Strain (production host): GS1993 (GLYA-, PHEA905, DELTA LACU169,STRA,THI, DELTAGLYA::MU, RECA-)
References: UniProt: P0A825, 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-FFO / N-[4-({[(6S)-2-amino-5-formyl-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid / [6S]-5-FORMYL-TETRAHYDROFOLATE / 6S-FOLINIC ACID


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


Mass: 18.015 Da / Num. of mol.: 388 / 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: 3.39 Å3/Da / Density % sol: 63.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.2
Details: 2M POTASSIUM PHOSPHATE, pH 7.2, VAPOR DIFFUSION, temperature 293.0K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Stover, P., (1993) J.Mol.Biol., 230, 1094.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
125 %satpotassium phosphate1drop
230-50 mg/mlenzyme1drop
340 %satpotassium phosphate1reservoir
4PEG4001reservoiror glycerol or 1,2,3-heptanetriol

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jun 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→91 Å / Num. all: 93964 / Num. obs: 93782 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 43.5 Å2 / Rmerge(I) obs: 0.23 / Net I/σ(I): 7.1
Reflection shellResolution: 2.41→2.49 Å / Redundancy: 4 % / Rmerge(I) obs: 1 / % possible all: 100
Reflection
*PLUS
Num. obs: 83968 / % possible obs: 89 % / Biso Wilson estimate: 44 Å2
Reflection shell
*PLUS
% possible obs: 78 % / Mean I/σ(I) obs: 1.22

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 2.4→20 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 1937647.26 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2.2 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.196 8284 10 %RANDOM
Rwork0.174 ---
obs0.174 82807 88 %-
all-93980 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.55 Å2 / ksol: 0.321 e/Å3
Displacement parametersBiso mean: 36.2 Å2
Baniso -1Baniso -2Baniso -3
1-1.7 Å20 Å20.11 Å2
2---6.77 Å20 Å2
3---5.07 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12620 0 196 388 13204
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.07
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.11.5
X-RAY DIFFRACTIONc_mcangle_it3.072
X-RAY DIFFRACTIONc_scbond_it23.792
X-RAY DIFFRACTIONc_scangle_it21.312.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.299 1069 10.1 %
Rwork0.283 9498 -
obs--67.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3PLP.PARPLP.TOP
X-RAY DIFFRACTION4PATCH_PLP.PARPATCH_PLP.TOP
X-RAY DIFFRACTION5FFO.PARFFO.TOP
Software
*PLUS
Name: 'CNS' / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 73994 / Num. reflection Rfree: 8242
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg2.07

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