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- PDB-6tgh: SHMT from Streptococcus thermophilus Tyr55Thr variant in complex ... -

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Basic information

Entry
Database: PDB / ID: 6tgh
TitleSHMT from Streptococcus thermophilus Tyr55Thr variant in complex with D-Serine both as external aldimine and as non-covalent 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 / tetrahydrofolate interconversion / methyltransferase activity / pyridoxal phosphate binding / methylation / cytoplasm
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 / Chem-EVM / PYRIDOXAL-5'-PHOSPHATE / Serine hydroxymethyltransferase / Serine hydroxymethyltransferase
Similarity search - Component
Biological speciesStreptococcus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsPetrillo, G. / Hernandez, K. / Bujons, J. / Clapes, P. / Uson, I.
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 15, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 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
B: Serine hydroxymethyltransferase
D: Serine hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,21913
Polymers179,7794
Non-polymers1,4409
Water6,864381
1
A: Serine hydroxymethyltransferase
C: Serine hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,6217
Polymers89,8902
Non-polymers7315
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7420 Å2
ΔGint-46 kcal/mol
Surface area27530 Å2
MethodPISA
2
B: Serine hydroxymethyltransferase
D: Serine hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,5986
Polymers89,8902
Non-polymers7084
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7590 Å2
ΔGint-62 kcal/mol
Surface area27590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)200.795, 112.930, 131.918
Angle α, β, γ (deg.)90.000, 93.100, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 4 molecules ACBD

#1: Protein
Serine hydroxymethyltransferase / / Serine methylase


Mass: 44944.758 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

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Non-polymers , 5 types, 390 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EVM / L-Serine, N-[[3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]-4-pyridinyl]methylene]


Mass: 333.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H14N2O8P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-DSN / D-SERINE / Serine


Type: D-peptide linking / Mass: 105.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 381 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 4.21 Å3/Da / Density % sol: 70.81 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: PLP 0.1 mm D-Serine 100 mm cacodylate 0.1 M, pH 6.5 sodium citrate 0.85 M

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9798 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: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.1→98 Å / Num. obs: 165927 / % possible obs: 99.3 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.9
Reflection shellResolution: 2.2→2.2 Å / Rmerge(I) obs: 0.05 / Num. unique obs: 157619

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WXB

4wxb


Resolution: 2.12→47.76 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.928 / SU B: 8.021 / SU ML: 0.192 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.179 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2836 8296 5 %RANDOM
Rwork0.2368 ---
obs0.2391 157619 99.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 144.82 Å2 / Biso mean: 55.166 Å2 / Biso min: 26.61 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å2-0.02 Å2
2--0.26 Å20 Å2
3----0.33 Å2
Refinement stepCycle: final / Resolution: 2.12→47.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12476 0 91 381 12948
Biso mean--73.1 55.54 -
Num. residues----1640
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01312838
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711920
X-RAY DIFFRACTIONr_angle_refined_deg1.6471.64417444
X-RAY DIFFRACTIONr_angle_other_deg1.2931.57627678
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.53251642
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.12823.616614
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.677152100
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4741556
X-RAY DIFFRACTIONr_chiral_restr0.0710.21696
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214552
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022498
LS refinement shellResolution: 2.12→2.173 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.478 596 -
Rwork0.446 11336 -
obs--96.81 %

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