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- PDB-6ti4: SHMT from Streptococcus thermophilus Tyr55Ser variant in complex ... -

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Basic information

Entry
Database: PDB / ID: 6ti4
TitleSHMT from Streptococcus thermophilus Tyr55Ser variant in complex with PLP/D-Serine/Lys230 gem diamine complex
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 / serine binding / L-serine catabolic process / tetrahydrofolate interconversion / cobalt ion binding / folic acid metabolic process / pyridoxal phosphate binding / zinc ion binding ...glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / serine binding / L-serine catabolic process / tetrahydrofolate interconversion / cobalt ion binding / folic acid metabolic process / pyridoxal phosphate binding / zinc ion binding / 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 / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Chem-O3Z / Serine hydroxymethyltransferase / Serine hydroxymethyltransferase
Similarity search - Component
Biological speciesStreptococcus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 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: Crystal Structure of Y55S Serine Hydroxymethyltransferase variant from Streptococcus thermophilus in complex with gem-diamine intermediate of D-serine
Authors: Petrillo, G. / Hernandez, K. / Bujons, J. / Clapes, P. / Uson, I.
History
DepositionNov 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _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_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)91,0057
Polymers90,1242
Non-polymers8815
Water9,440524
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7340 Å2
ΔGint-51 kcal/mol
Surface area27780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.782, 114.782, 192.833
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-905-

HOH

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Components

#1: Protein Serine hydroxymethyltransferase / Serine methylase


Mass: 45061.926 Da / Num. of mol.: 2
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: Q5M4W1*PLUS, glycine hydroxymethyltransferase
#2: 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
#3: Chemical ChemComp-O3Z / (2~{R})-2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]-3-oxidanyl-propanoic acid


Mass: 336.235 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H17N2O8P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 524 / 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: 3.52 Å3/Da / Density % sol: 65.09 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: PLP 0.1M D-serine 100mM Cacodylate 0.1M ph 6.5 Sodium citrate 1M

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9697 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: 0.9697 Å / Relative weight: 1
ReflectionResolution: 1.93→98.63 Å / Num. obs: 92342 / % possible obs: 99.94 % / Redundancy: 2.98 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.16
Reflection shellResolution: 1.93→1.98 Å / Rmerge(I) obs: 0.07 / Num. unique obs: 6782

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
XPREPdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XWG

4xwg


Resolution: 1.93→98.63 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.965 / SU B: 3.041 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1907 4774 4.9 %RANDOM
Rwork0.1639 ---
obs0.1653 92342 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 123.23 Å2 / Biso mean: 42.213 Å2 / Biso min: 25.27 Å2
Baniso -1Baniso -2Baniso -3
1-2.06 Å2-0 Å2-0 Å2
2--2.06 Å2-0 Å2
3----4.12 Å2
Refinement stepCycle: final / Resolution: 1.93→98.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6236 0 57 524 6817
Biso mean--44.81 49.12 -
Num. residues----820
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0136419
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175962
X-RAY DIFFRACTIONr_angle_refined_deg1.7871.6458712
X-RAY DIFFRACTIONr_angle_other_deg1.4821.57813846
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5755819
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.30823.595306
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.204151048
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0391528
X-RAY DIFFRACTIONr_chiral_restr0.0910.2845
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027235
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021247
LS refinement shellResolution: 1.93→1.98 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 316 -
Rwork0.285 6782 -
all-7098 -
obs--99.65 %

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