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- PDB-6yrw: SHMT from Streptococcus thermophilus Tyr55Ser variant as internal... -

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Basic information

Entry
Database: PDB / ID: 6yrw
TitleSHMT from Streptococcus thermophilus Tyr55Ser variant as internal aldimine and as non-covalent complex with D-Ser
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-SERINE / PYRIDOXAL-5'-PHOSPHATE / Serine hydroxymethyltransferase / Serine hydroxymethyltransferase
Similarity search - Component
Biological speciesStreptococcus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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
DepositionApr 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 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)181,84114
Polymers180,2484
Non-polymers1,59310
Water6,774376
1
A: Serine hydroxymethyltransferase
C: Serine hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,9207
Polymers90,1242
Non-polymers7975
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8030 Å2
ΔGint-45 kcal/mol
Surface area27900 Å2
MethodPISA
2
B: Serine hydroxymethyltransferase
D: Serine hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,9207
Polymers90,1242
Non-polymers7975
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8080 Å2
ΔGint-44 kcal/mol
Surface area27900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)199.956, 113.657, 132.479
Angle α, β, γ (deg.)90.000, 94.130, 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-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-DSN / D-SERINE


Type: D-peptide linking / Mass: 105.093 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H7NO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 376 / 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: 4.24 Å3/Da / Density % sol: 70.97 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: PLP 5mM D-serine 100mM Cacodylate 0.1M ph 6.5 Sodium citrate 0.85M

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.9697 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9697 Å / Relative weight: 1
ReflectionResolution: 2.33→47.85 Å / Num. obs: 80329 / % possible obs: 76.01 % / Redundancy: 1.59 % / CC1/2: 0.95 / Net I/σ(I): 41.89
Reflection shellResolution: 2.5→2.565 Å / Num. unique obs: 73924 / CC1/2: 0.95

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
XPREPdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WXG

4wxg


Resolution: 2.5→47.85 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.919 / SU B: 8.8 / SU ML: 0.181 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.376 / ESU R Free: 0.264 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2265 3838 4.9 %RANDOM
Rwork0.1763 ---
obs0.1788 73924 76.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 137.12 Å2 / Biso mean: 40.372 Å2 / Biso min: 3.2 Å2
Baniso -1Baniso -2Baniso -3
1--2.82 Å20 Å2-3.26 Å2
2---0.13 Å20 Å2
3---3.38 Å2
Refinement stepCycle: final / Resolution: 2.5→47.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12472 0 100 376 12948
Biso mean--42.1 33.02 -
Num. residues----1640
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01312817
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711910
X-RAY DIFFRACTIONr_angle_refined_deg1.5871.64217399
X-RAY DIFFRACTIONr_angle_other_deg1.2861.57427652
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.20851635
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.00223.595612
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.187152096
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2461556
X-RAY DIFFRACTIONr_chiral_restr0.0660.21688
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214521
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022487
LS refinement shellResolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 99 -
Rwork0.373 1783 -
all-1882 -
obs--25.01 %

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