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

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Basic information

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


serine binding / L-serine catabolic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate interconversion / cobalt ion binding / folic acid metabolic process / methyltransferase activity / pyridoxal phosphate binding ...serine binding / L-serine catabolic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate interconversion / cobalt ion binding / folic acid metabolic process / methyltransferase activity / pyridoxal phosphate binding / methylation / zinc ion 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
DI(HYDROXYETHYL)ETHER / Serine hydroxymethyltransferase
Similarity search - Component
Biological speciesAphanothece halophytica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 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)49,4517
Polymers48,8841
Non-polymers5676
Water8,521473
1
A: Serine hydroxymethyltransferase
hetero molecules

A: Serine hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,90114
Polymers97,7682
Non-polymers1,13312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area10360 Å2
ΔGint-56 kcal/mol
Surface area28520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.383, 94.383, 134.466
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-1061-

HOH

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Components

#1: Protein Serine hydroxymethyltransferase / Serine methylase


Mass: 48884.152 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.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 473 / 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: 3.54 Å3/Da / Density % sol: 65.22 %
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

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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: 1.77→81.74 Å / Num. obs: 67717 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 11.3 % / CC1/2: 0.999 / Rrim(I) all: 0.092 / Net I/σ(I): 15.8
Reflection shellResolution: 1.77→1.88 Å / Redundancy: 11.3 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 10631 / CC1/2: 0.768 / Rrim(I) all: 1.09 / % possible all: 98.1

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Processing

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

6ymd


Resolution: 1.77→81.74 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.962 / SU B: 3.172 / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.074
Details: HYDROGENS WERE ADDED IN THE RIDING POSITIONS DURING REFINEMENT; U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1747 1016 1.5 %RANDOM
Rwork0.1411 ---
obs0.1416 66654 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 90.52 Å2 / Biso mean: 32.036 Å2 / Biso min: 19.93 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20.17 Å2-0 Å2
2--0.35 Å20 Å2
3----1.12 Å2
Refinement stepCycle: final / Resolution: 1.77→81.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3268 0 37 473 3778
Biso mean--56.18 45.74 -
Num. residues----425
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0143385
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173058
X-RAY DIFFRACTIONr_angle_refined_deg1.7021.6714587
X-RAY DIFFRACTIONr_angle_other_deg1.1331.6577181
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1425430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.24223.176170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.79715549
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2761518
X-RAY DIFFRACTIONr_chiral_restr0.0980.2444
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023815
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02589
LS refinement shellResolution: 1.771→1.817 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.215 71 -
Rwork0.252 4685 -
all-4756 -
obs--95.85 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.05730.0297-0.07120.083-0.10110.3576-0.00380.03630.00650.03050.0153-0.0013-0.080.0052-0.01150.03810.00890.00110.0756-0.00080.058424.908246.657164.5371
20.19160.0238-0.070.2099-0.03840.2788-0.03760.0916-0.0160.0450.0879-0.01130.0273-0.072-0.05040.0212-0.0035-0.00580.0909-0.010.058214.893728.523651.9165
30.57880.0014-0.330.0076-0.0080.1951-0.01120.055-0.0299-0.0043-0.0218-0.01740.0094-0.01440.03290.00370.00440.01610.08460.01180.072541.074632.645646.2059
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 87
2X-RAY DIFFRACTION2A88 - 281
3X-RAY DIFFRACTION3A282 - 426

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