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- PDB-6ti3: Apo-SHMT from Streptococcus thermophilus Tyr55Ser variant in comp... -

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Basic information

Entry
Database: PDB / ID: 6ti3
TitleApo-SHMT from Streptococcus thermophilus Tyr55Ser variant in complex with D-Threonine
ComponentsSerine hydroxymethyltransferase
KeywordsTRANSFERASE / Pyridoxal phosphate / X-ray crystallography / hydroxymethyltransferase / proton abstraction / tetrahydrofolate-independent
Function / homology
Function and homology information


glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate interconversion / pyridoxal phosphate binding / cytosol
Similarity search - Function
Serine hydroxymethyltransferase, pyridoxal phosphate binding site / Serine hydroxymethyltransferase pyridoxal-phosphate attachment site. / : / Serine hydroxymethyltransferase / Serine hydroxymethyltransferase-like domain / Serine hydroxymethyltransferase / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
D-THREONINE / Serine hydroxymethyltransferase / Serine hydroxymethyltransferase
Similarity search - Component
Biological speciesStreptococcus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsPetrillo, G. / Hernandez, K. / Bujons, J. / Clapes, P. / Uson, I.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and Competitiveness Spain
CitationJournal: To Be Published
Title: Structural insights into nucleophile substrate specificity in variants of N-Serine hydroxymethyltransferase from Streptococcus thermophilus
Authors: Petrillo, G. / Hernandez, K. / Bujons, J. / Clapes, P. / Uson, I.
History
DepositionNov 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine hydroxymethyltransferase
C: Serine hydroxymethyltransferase
B: Serine hydroxymethyltransferase
D: Serine hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,02312
Polymers180,2484
Non-polymers7768
Water14,862825
1
A: Serine hydroxymethyltransferase
C: Serine hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,5466
Polymers90,1242
Non-polymers4224
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7070 Å2
ΔGint-44 kcal/mol
Surface area28010 Å2
MethodPISA
2
B: Serine hydroxymethyltransferase
D: Serine hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,4776
Polymers90,1242
Non-polymers3534
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7090 Å2
ΔGint-54 kcal/mol
Surface area28050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)200.393, 113.692, 133.147
Angle α, β, γ (deg.)90.000, 94.510, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Serine hydroxymethyltransferase / Serine methylase


Mass: 45061.926 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus thermophilus (bacteria) / Gene: glyA, CDA68_00974, DID82_07515 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5MCK9, UniProt: Q5M0B4*PLUS, glycine hydroxymethyltransferase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-DTH / D-THREONINE


Type: D-peptide linking / Mass: 119.119 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H9NO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 825 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 4.27 Å3/Da / Density % sol: 71.17 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: PLP 0.1M D-threonine 5mM Cacodylate 0.1M ph 6.5 Sodium citrate 1.2M

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.933 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.96→100.09 Å / Num. obs: 208923 / % possible obs: 98.78 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.8
Reflection shellResolution: 1.965→2.016 Å / Rmerge(I) obs: 0.09 / Num. unique obs: 15299

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
XPREPdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WXG

4wxg


Resolution: 1.96→100.09 Å / Cor.coef. Fo:Fc: 0.968 / SU B: 2.792 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflection
Rwork0.1806 --
obs0.1806 208923 98.78 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 127.81 Å2 / Biso mean: 42.781 Å2 / Biso min: 20.35 Å2
Baniso -1Baniso -2Baniso -3
1--2.61 Å2-0 Å2-2.12 Å2
2--0.06 Å2-0 Å2
3---2.85 Å2
Refinement stepCycle: final / Resolution: 1.96→100.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12472 0 51 825 13348
Biso mean--51.66 49.28 -
Num. residues----1640
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01512789
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711704
X-RAY DIFFRACTIONr_angle_refined_deg1.8841.75617359
X-RAY DIFFRACTIONr_angle_other_deg0.6341.73927360
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.45451642
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.07722.191502
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.323151876
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7251556
X-RAY DIFFRACTIONr_chiral_restr0.0970.21699
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02114508
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022270
LS refinement shellResolution: 1.965→2.016 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.311 15299 -
obs--97.98 %

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