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- PDB-9boh: Room-temperature X-ray structure of Thermus Thermophilus serine h... -

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Basic information

Entry
Database: PDB / ID: 9boh
TitleRoom-temperature X-ray structure of Thermus Thermophilus serine hydroxymethyltransferase (SHMT) with PLP-glycine external aldimine and 5-formyltetrahydrofolate (folinic acid)
ComponentsSerine hydroxymethyltransferase
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 L-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 / Serine hydroxymethyltransferase
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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 3, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)89,2676
Polymers88,2972
Non-polymers9704
Water7,368409
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8960 Å2
ΔGint-82 kcal/mol
Surface area25860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.785, 83.344, 95.538
Angle α, β, γ (deg.)90.00, 91.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Serine hydroxymethyltransferase / SHMT / Serine methylase


Mass: 44148.562 Da / Num. of mol.: 2
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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-A1AQW / (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)glycine


Mass: 304.193 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N2O7P / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 409 / 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: 2.65 Å3/Da / Density % sol: 53.57 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 40 mM NaOAc pH 5.5, 0.5 M Gly, 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: Nov 22, 2022 / 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: 2→29.74 Å / Num. obs: 61808 / % possible obs: 99.1 % / Redundancy: 5.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.035 / Rpim(I) all: 0.024 / Net I/σ(I): 27.4
Reflection shellResolution: 2→2.05 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.085 / Mean I/σ(I) obs: 15.1 / Num. unique obs: 4473 / CC1/2: 0.993 / Rpim(I) all: 0.059 / % possible all: 97.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
CrysalisProdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→27.85 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 14.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1547 2938 4.76 %
Rwork0.1306 --
obs0.1317 61738 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→27.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6220 0 64 409 6693
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0156472
X-RAY DIFFRACTIONf_angle_d1.3648778
X-RAY DIFFRACTIONf_dihedral_angle_d15.3342442
X-RAY DIFFRACTIONf_chiral_restr0.078960
X-RAY DIFFRACTIONf_plane_restr0.0371160
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.030.17981120.15072767X-RAY DIFFRACTION97
2.03-2.070.19131280.13572751X-RAY DIFFRACTION99
2.07-2.110.18151160.13742822X-RAY DIFFRACTION98
2.11-2.150.18891280.13932727X-RAY DIFFRACTION98
2.15-2.190.1811230.1282822X-RAY DIFFRACTION99
2.19-2.240.14861320.12732775X-RAY DIFFRACTION99
2.24-2.290.17421430.13132752X-RAY DIFFRACTION99
2.29-2.350.16851630.13122794X-RAY DIFFRACTION99
2.35-2.410.16421730.13862718X-RAY DIFFRACTION99
2.41-2.480.17461400.13782817X-RAY DIFFRACTION99
2.48-2.560.18851390.14782821X-RAY DIFFRACTION99
2.56-2.650.19021510.14612769X-RAY DIFFRACTION99
2.65-2.760.19351470.14242828X-RAY DIFFRACTION100
2.76-2.880.1571720.1422772X-RAY DIFFRACTION100
2.88-3.040.161490.13842790X-RAY DIFFRACTION100
3.04-3.230.14511510.13572831X-RAY DIFFRACTION100
3.23-3.470.14131630.12942827X-RAY DIFFRACTION100
3.47-3.820.11791360.11162830X-RAY DIFFRACTION100
3.82-4.370.12541170.1062879X-RAY DIFFRACTION100
4.37-5.50.11651400.1192849X-RAY DIFFRACTION100
5.5-27.850.14451150.13532859X-RAY DIFFRACTION97

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