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- PDB-8ssy: Room-temperature X-ray structure of Thermus thermophilus serine h... -

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Basic information

Entry
Database: PDB / ID: 8ssy
TitleRoom-temperature X-ray structure of Thermus thermophilus serine hydroxymethyltransferase (SHMT) bound with D-Ser in a pseudo-Michaelis complex
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 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
D-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)R01GM137008-01A1 United States
CitationJournal: Commun Chem / Year: 2023
Title: Revealing protonation states and tracking substrate in serine hydroxymethyltransferase with room-temperature X-ray and neutron crystallography.
Authors: Drago, V.N. / Campos, C. / Hooper, M. / Collins, A. / Gerlits, O. / Weiss, K.L. / Blakeley, M.P. / Phillips, R.S. / Kovalevsky, A.
History
DepositionMay 9, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)89,5574
Polymers89,3562
Non-polymers2012
Water8,395466
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7580 Å2
ΔGint-60 kcal/mol
Surface area26240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.907, 83.473, 95.696
Angle α, β, γ (deg.)90.00, 91.69, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Serine hydroxymethyltransferase / SHMT / Serine methylase


Mass: 44678.020 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-DSN / D-SERINE


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


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 466 / 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: 2.63 Å3/Da / Density % sol: 53.26 %
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 with 40 mM NaOAc pH 5.5, 0.5 M D-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: 1.5418 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Jun 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→100 Å / Num. obs: 85843 / % possible obs: 100 % / Redundancy: 13.3 % / CC1/2: 0.998 / Rpim(I) all: 0.02 / Net I/σ(I): 36
Reflection shellResolution: 1.8→1.86 Å / Num. unique obs: 8588 / CC1/2: 0.92 / Rpim(I) all: 0.132

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
CrysalisProdata reduction
CrysalisProdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→29.44 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 15.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1634 8388 4.97 %
Rwork0.1318 --
obs0.1333 85779 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→29.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6248 0 12 466 6726
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.026518
X-RAY DIFFRACTIONf_angle_d1.6078850
X-RAY DIFFRACTIONf_dihedral_angle_d14.1472468
X-RAY DIFFRACTIONf_chiral_restr0.125967
X-RAY DIFFRACTIONf_plane_restr0.0161172
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.22162510.19535389X-RAY DIFFRACTION99
1.82-1.840.20432570.18875360X-RAY DIFFRACTION100
1.84-1.860.21272490.18025342X-RAY DIFFRACTION100
1.86-1.890.21542630.16755384X-RAY DIFFRACTION100
1.89-1.910.19143030.15465273X-RAY DIFFRACTION100
1.91-1.940.1742770.14875367X-RAY DIFFRACTION100
1.94-1.970.192930.14565379X-RAY DIFFRACTION100
1.97-20.17972660.14275325X-RAY DIFFRACTION100
2-2.030.19582880.13715337X-RAY DIFFRACTION100
2.03-2.060.1873030.13925289X-RAY DIFFRACTION100
2.06-2.10.18052790.1425375X-RAY DIFFRACTION100
2.1-2.130.19373390.14335311X-RAY DIFFRACTION100
2.13-2.180.20262910.14725361X-RAY DIFFRACTION100
2.18-2.220.15552990.13615304X-RAY DIFFRACTION100
2.22-2.270.17122730.13365424X-RAY DIFFRACTION100
2.27-2.320.15962760.1295262X-RAY DIFFRACTION100
2.32-2.380.16842880.14165353X-RAY DIFFRACTION100
2.38-2.440.17783160.13845332X-RAY DIFFRACTION100
2.44-2.510.19432680.13975289X-RAY DIFFRACTION100
2.51-2.60.16832850.13885367X-RAY DIFFRACTION100
2.6-2.690.18113250.13845324X-RAY DIFFRACTION100
2.69-2.80.14573280.13295299X-RAY DIFFRACTION100
2.8-2.920.16142600.13365348X-RAY DIFFRACTION100
2.92-3.080.18882730.13595399X-RAY DIFFRACTION100
3.08-3.270.16952680.13495333X-RAY DIFFRACTION100
3.27-3.520.1462540.12865380X-RAY DIFFRACTION100
3.52-3.880.12412250.10655360X-RAY DIFFRACTION100
3.88-4.430.12072690.10125391X-RAY DIFFRACTION100
4.43-5.580.13842640.10995362X-RAY DIFFRACTION100
5.58-29.440.12642580.11615276X-RAY DIFFRACTION98

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