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- PDB-9bow: X-ray structure of Thermus thermophilus serine hydroxymethyltrans... -

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Basic information

Entry
Database: PDB / ID: 9bow
TitleX-ray structure of Thermus thermophilus serine hydroxymethyltransferase with PLP-L-Ser external aldimine and 5-formyltetrahydrofolate (folinic acid)
Components(Serine hydroxymethyltransferase) x 2
KeywordsTRANSFERASE / PYRIDOXAL 5'-PHOSPHATE / PLP / FOLD TYPE 1 / ONE CARBON METABOLISM
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
Chem-FFO / Chem-KOU / SERINE / Serine hydroxymethyltransferase
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsDrago, V.N. / Kovalevsky, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM137008 United States
CitationJournal: Chem Sci / Year: 2024
Title: Universality of critical active site glutamate as an acid-base catalyst in serine hydroxymethyltransferase function.
Authors: Drago, V.N. / Phillips, R.S. / Kovalevsky, A.
History
DepositionMay 6, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)89,6307
Polymers88,5252
Non-polymers1,1055
Water14,880826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8930 Å2
ΔGint-60 kcal/mol
Surface area25570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.131, 82.814, 94.446
Angle α, β, γ (deg.)90.00, 91.58, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Serine hydroxymethyltransferase / SHMT / Serine methylase


Mass: 44376.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Gene: glyA, TTHA1524 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5SI56, glycine hydroxymethyltransferase
#2: Protein Serine hydroxymethyltransferase / SHMT / Serine methylase


Mass: 44148.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Gene: glyA, TTHA1524 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5SI56, glycine hydroxymethyltransferase

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Non-polymers , 5 types, 831 molecules

#3: Chemical ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-KOU / (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-serine


Mass: 334.219 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15N2O8P / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-FFO / N-[4-({[(6S)-2-amino-5-formyl-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid / [6S]-5-FORMYL-TETRAHYDROFOLATE / 6S-FOLINIC ACID


Mass: 473.439 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H23N7O7 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 826 / 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: 2.57 Å3/Da / Density % sol: 52.08 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 40 mM NaOAc pH 5.5, 1 M (NH4)2SO4, 0.5 M Li2SO4, soaked in 40 mM NaOAc pH 5.5, 0.5 M L-Ser, 15% PEG 4000

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5406 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Jan 10, 2023 / Details: Osmic VariMax
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 1.8→29.05 Å / Num. obs: 76390 / % possible obs: 92.2 % / Redundancy: 3.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.03 / Rpim(I) all: 0.026 / Net I/σ(I): 23.3
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.111 / Mean I/σ(I) obs: 7.6 / Num. unique obs: 2744 / CC1/2: 0.969 / Rpim(I) all: 0.105 / % possible all: 56.4

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
CrysalisProdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→29.05 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.07 / Phase error: 15.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1595 3838 5.03 %
Rwork0.1315 --
obs0.1329 76265 91.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→29.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6233 0 73 826 7132
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0146493
X-RAY DIFFRACTIONf_angle_d1.2458806
X-RAY DIFFRACTIONf_dihedral_angle_d13.0692442
X-RAY DIFFRACTIONf_chiral_restr0.084963
X-RAY DIFFRACTIONf_plane_restr0.0181160
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.186890.13491585X-RAY DIFFRACTION55
1.82-1.850.172740.13021755X-RAY DIFFRACTION60
1.85-1.870.1719970.12621935X-RAY DIFFRACTION66
1.87-1.90.17141130.13141995X-RAY DIFFRACTION70
1.9-1.930.18091170.1322226X-RAY DIFFRACTION75
1.93-1.960.18981140.13732412X-RAY DIFFRACTION84
1.96-1.990.18321490.13032684X-RAY DIFFRACTION91
1.99-2.020.16131500.12942798X-RAY DIFFRACTION96
2.02-2.060.15311530.12782837X-RAY DIFFRACTION99
2.06-2.10.16881550.13032864X-RAY DIFFRACTION99
2.1-2.140.16591430.12882916X-RAY DIFFRACTION99
2.14-2.190.18161400.12152880X-RAY DIFFRACTION99
2.19-2.240.14171230.12762963X-RAY DIFFRACTION99
2.24-2.30.1631650.12342853X-RAY DIFFRACTION99
2.3-2.360.1791770.12982852X-RAY DIFFRACTION99
2.36-2.430.16361640.13172895X-RAY DIFFRACTION100
2.43-2.510.16811480.13542914X-RAY DIFFRACTION100
2.51-2.60.16691630.13612889X-RAY DIFFRACTION100
2.6-2.70.17121450.13882886X-RAY DIFFRACTION100
2.7-2.820.19181600.13382904X-RAY DIFFRACTION99
2.82-2.970.1561590.13192925X-RAY DIFFRACTION99
2.97-3.160.16121320.13662906X-RAY DIFFRACTION99
3.16-3.40.171680.13912880X-RAY DIFFRACTION98
3.4-3.740.14981660.12792892X-RAY DIFFRACTION99
3.74-4.280.13571530.11872919X-RAY DIFFRACTION100
4.28-5.390.11151490.12342965X-RAY DIFFRACTION100
5.39-29.050.15371720.15582897X-RAY DIFFRACTION97

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