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- PDB-1eqb: X-RAY CRYSTAL STRUCTURE AT 2.7 ANGSTROMS RESOLUTION OF TERNARY CO... -

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Basic information

Entry
Database: PDB / ID: 1eqb
TitleX-RAY CRYSTAL STRUCTURE AT 2.7 ANGSTROMS RESOLUTION OF TERNARY COMPLEX BETWEEN THE Y65F MUTANT OF E-COLI SERINE HYDROXYMETHYLTRANSFERASE, GLYCINE AND 5-FORMYL TETRAHYDROFOLATE
ComponentsSERINE HYDROXYMETHYLTRANSFERASE
KeywordsTRANSFERASE / Functional mutant / hydroxymethyltransferase / aat-like fold / one carbon metabolism
Function / homology
Function and homology information


glycine catabolic process / L-allo-threonine aldolase activity / L-serine catabolic process / L-serine biosynthetic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate metabolic process / tetrahydrofolate interconversion / pyridoxal phosphate binding ...glycine catabolic process / L-allo-threonine aldolase activity / L-serine catabolic process / L-serine biosynthetic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate metabolic process / tetrahydrofolate interconversion / 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) ...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 / GLYCINE / PYRIDOXAL-5'-PHOSPHATE / Serine hydroxymethyltransferase / Serine hydroxymethyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.7 Å
AuthorsContestabile, R. / Angelaccio, S. / Bossa, F. / Wright, H.T. / Scarsdale, N. / Kazanina, G. / Schirch, V.
Citation
Journal: Biochemistry / Year: 2000
Title: Role of tyrosine 65 in the mechanism of serine hydroxymethyltransferase.
Authors: Contestabile, R. / Angelaccio, S. / Bossa, F. / Wright, H.T. / Scarsdale, N. / Kazanina, G. / Schirch, V.
#1: Journal: J.Mol.Biol. / Year: 2000
Title: Crystal Structure at 2.4 Angstrom 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
DepositionApr 3, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3May 7, 2014Group: Other
Revision 1.4Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)184,60916
Polymers181,4264
Non-polymers3,18312
Water5,170287
1
A: SERINE HYDROXYMETHYLTRANSFERASE
B: SERINE HYDROXYMETHYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,3048
Polymers90,7132
Non-polymers1,5916
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10880 Å2
ΔGint-56 kcal/mol
Surface area26290 Å2
MethodPISA
2
C: SERINE HYDROXYMETHYLTRANSFERASE
D: SERINE HYDROXYMETHYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,3048
Polymers90,7132
Non-polymers1,5916
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10900 Å2
ΔGint-58 kcal/mol
Surface area26470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.740, 172.480, 95.410
Angle α, β, γ (deg.)90.00, 104.28, 90.00
Int Tables number4
Space group name H-MP1211
DetailsBiological assembly is a dimer composed of two monomers. The assymetric unit contains two such dimers. One dimer consists of monomers A + B and the other consists of monomers C + D.

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Components

#1: Protein
SERINE HYDROXYMETHYLTRANSFERASE


Mass: 45356.477 Da / Num. of mol.: 4 / Mutation: Y65F
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): GS245
References: UniProt: P00477, UniProt: P0A825*PLUS, glycine hydroxymethyltransferase
#2: Chemical
ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H5NO2
#3: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 3.42 Å3/Da / Density % sol: 63.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.2
Details: 2M K3PO4, pH 7.2, VAPOR DIFFUSION, temperature 298K
Crystal grow
*PLUS
Method: unknown

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Mar 26, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→92 Å / Num. all: 66775 / Num. obs: 63328 / % possible obs: 94.8 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 48.8 Å2 / Rmerge(I) obs: 0.28 / Net I/σ(I): 5.53
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 4.9 % / Rmerge(I) obs: 1 / Num. unique all: 2865 / % possible all: 86.1
Reflection shell
*PLUS
% possible obs: 96.1 % / Mean I/σ(I) obs: 1.09

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 2.7→20 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2118892.63 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.236 6375 10.1 %RANDOM
Rwork0.205 ---
obs0.205 62997 94.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.76 Å2 / ksol: 0.307 e/Å3
Displacement parametersBiso mean: 36.8 Å2
Baniso -1Baniso -2Baniso -3
1-3.63 Å20 Å23.19 Å2
2---5.68 Å20 Å2
3---2.05 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12659 0 216 287 13162
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_improper_angle_d2.09
Refine LS restraints NCSRms dev position: 0.03 Å / Weight position: 150
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.334 964 10.1 %
Rwork0.298 8574 -
obs--86.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PLP.PARPLP.TOP
X-RAY DIFFRACTION3PATCH_PLP.PPATCH_PLP.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION5FFO.PARFFO.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg2.09

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