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- PDB-6ymf: Crystal structure of serine hydroxymethyltransferase from Aphanot... -

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Basic information

Entry
Database: PDB / ID: 6ymf
TitleCrystal structure of serine hydroxymethyltransferase from Aphanothece halophytica in the PLP-Serine external aldimine state
ComponentsSerine hydroxymethyltransferase
KeywordsTRANSFERASE / SERINE BIOSYNTHESIS / GLYCINE / PLP / ONE-CARBON METABOLISM / TETRAHYDROFOLATE
Function / homology
Function and homology information


glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate interconversion / methyltransferase activity / pyridoxal phosphate binding / methylation / 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-PLS / Serine hydroxymethyltransferase
Similarity search - Component
Biological speciesAphanothece halophytica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsRuszkowski, M. / Sekula, B. / Nogues, I. / Tramonti, A. / Angelaccio, S. / Contestabile, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)Intramural Research Program United States
CitationJournal: Int.J.Biol.Macromol. / Year: 2020
Title: Structural and kinetic properties of serine hydroxymethyltransferase from the halophytic cyanobacterium Aphanothece halophytica provide a rationale for salt tolerance.
Authors: Nogues, I. / Tramonti, A. / Angelaccio, S. / Ruszkowski, M. / Sekula, B. / Contestabile, R.
History
DepositionApr 8, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jun 17, 2020Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.3Jan 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,96711
Polymers48,6561
Non-polymers1,31110
Water7,224401
1
A: Serine hydroxymethyltransferase
hetero molecules

A: Serine hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,93522
Polymers97,3122
Non-polymers2,62320
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area12110 Å2
ΔGint-68 kcal/mol
Surface area26990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.888, 93.888, 134.683
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Serine hydroxymethyltransferase / Serine methylase


Mass: 48656.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aphanothece halophytica (bacteria) / Gene: glyrA, glyA / Plasmid: pET28b(+) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: I7H6W6, glycine hydroxymethyltransferase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PLS / [3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-SERINE / PYRIDOXYL-SERINE-5-MONOPHOSPHATE


Mass: 336.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H17N2O8P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 401 / 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: 65.08 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.05 M citric acid, 0.05 M BIS-TRIS propane at pH 5.0 and 16% polyethylene glycol 3350 cocrystallized with 50 mM L-serine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 17, 2018
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.63→44.89 Å / Num. obs: 86052 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 11.3 % / CC1/2: 1 / Rrim(I) all: 0.045 / Net I/σ(I): 29.5
Reflection shellResolution: 1.63→1.73 Å / Redundancy: 11.3 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 13719 / CC1/2: 0.847 / Rrim(I) all: 1.098 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YMD

6ymd


Resolution: 1.63→44.89 Å / Cor.coef. Fo:Fc: 0.988 / Cor.coef. Fo:Fc free: 0.985 / SU B: 2.525 / SU ML: 0.035 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.047 / ESU R Free: 0.044
Details: HYDROGENS WERE ADDED IN THE RIDING POSITIONS DURING REFINEMENT; U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1298 1033 1.2 %RANDOM
Rwork0.1064 ---
obs0.1067 85018 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 152.37 Å2 / Biso mean: 35.566 Å2 / Biso min: 18.94 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å2-0.2 Å2-0 Å2
2---0.41 Å20 Å2
3---1.32 Å2
Refinement stepCycle: final / Resolution: 1.63→44.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3207 0 86 401 3694
Biso mean--55.06 52.96 -
Num. residues----418
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0143390
X-RAY DIFFRACTIONr_bond_other_d0.0040.0173072
X-RAY DIFFRACTIONr_angle_refined_deg1.8131.6794584
X-RAY DIFFRACTIONr_angle_other_deg1.1681.6697221
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3015429
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.84923.256172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.25715558
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5061518
X-RAY DIFFRACTIONr_chiral_restr0.10.2443
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023797
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02586
X-RAY DIFFRACTIONr_rigid_bond_restr4.89936462
X-RAY DIFFRACTIONr_sphericity_free38.7055245
X-RAY DIFFRACTIONr_sphericity_bonded26.15656554
LS refinement shellResolution: 1.63→1.672 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 75 -
Rwork0.276 6159 -
all-6234 -
obs--98.55 %

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