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- PDB-8sui: Joint X-ray/neutron structure of Thermus thermophilus serine hydr... -

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Basic information

Entry
Database: PDB / ID: 8sui
TitleJoint X-ray/neutron structure of Thermus thermophilus serine hydroxymethyltransferase (TthSHMT) in internal aldimine state with L-Ser bound in a pre-Michalis 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 / serine binding / L-serine catabolic process / tetrahydrofolate interconversion / cobalt ion binding / folic acid metabolic process / pyridoxal phosphate binding / 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
DEUTERATED WATER / SERINE / Serine hydroxymethyltransferase
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 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 12, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)89,6535
Polymers89,3562
Non-polymers2973
Water7,134396
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8140 Å2
ΔGint-95 kcal/mol
Surface area26180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.807, 83.334, 95.568
Angle α, β, γ (deg.)90.00, 91.68, 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#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-DOD / water


Mass: 18.015 Da / Num. of mol.: 396 / Source method: isolated from a natural source / Formula: D2O
Has ligand of interestY

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.04 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 40 mM NaOAc pH 5.5, 1.0 M (NH4)2SO4, and 0.5 M Li2SO4

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
12931N
22931N
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SPALLATION SOURCEORNL Spallation Neutron Source MANDI12-4.16
ROTATING ANODERIGAKU MICROMAX-007 HF21.54
Detector
TypeIDDetectorDateDetails
ORNL ANGER CAMERA1AREA DETECTORAug 10, 2022
DECTRIS EIGER R 4M2PIXELDec 6, 2022Osmic Varimax
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1NONELAUELneutron1
2NONESINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
121
24.161
31.541
Reflection

Entry-ID: 8SUI

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)CC1/2Rmerge(I) obsRpim(I) allDiffraction-IDNet I/σ(I)
2.3-14.4339816975.30.9180.2280.097110.3
2-95.596255299.94.40.9910.1070.059213.1
Reflection shell
Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allDiffraction-ID
2.3-2.3895.94.40.2454.739200.6380.1151
2-2.0799.44.20.4592.762270.6670.2582

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Processing

Software
NameVersionClassification
nCNS1.0.8refinement
CrysalisProdata reduction
CrysalisProdata scaling
PHASERphasing
Mantiddata reduction
SCALAdata scaling
Refinement

Biso max: 76.1 Å2 / Biso mean: 17.68 Å2 / Biso min: 4 Å2 / % reflection Rfree: 5 % / R Free selection details: random / Cross valid method: FREE R-VALUE / σ(F): 2.5 / Method to determine structure: MOLECULAR REPLACEMENT / Stereochemistry target values: Joint X-ray/neutron ML / Solvent model: CNS bulk solvent model used / Bsol: 27.4882 Å2 / ksol: 0.642037 e/Å3

Resolution (Å)Refine-IDRfactor RfreeRfactor Rfree errorRfactor RworkNum. reflection RfreeNum. reflection RworkNum. reflection obs% reflection obs (%)Diffraction-ID
2.3-40NEUTRON DIFFRACTION0.2210.0070.20419813773139712971
2-40X-RAY DIFFRACTION0.1830.0030.1662853534785633193.72
Refine analyze
Refine-ID#notag 0
NEUTRON DIFFRACTION
FreeObs
Luzzati coordinate error0.360.34
Luzzati d res low-5
Luzzati sigma a0.390.38
Luzzati d res high-2.3
X-RAY DIFFRACTION
FreeObs
Luzzati coordinate error0.190.17
Luzzati d res low-5
Luzzati sigma a0.190.16
Luzzati d res high-2
Refine funct minimized
Refine-IDType
NEUTRON DIFFRACTIONJoint X-ray/neutron ML
X-RAY DIFFRACTIONJoint X-ray/neutron ML
Refinement stepCycle: LAST / Resolution: 2.3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6250 0 17 396 6663
Refine LS restraints
Refine-IDTypeDev ideal
NEUTRON DIFFRACTIONx_bond_d0.007
NEUTRON DIFFRACTIONx_angle_deg1
NEUTRON DIFFRACTIONx_torsion_deg17.3
NEUTRON DIFFRACTIONx_torsion_impr_deg0.76
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1
X-RAY DIFFRACTIONx_torsion_deg17.3
X-RAY DIFFRACTIONx_torsion_impr_deg0.76
LS refinement shell

Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRefine-IDRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.3-2.40.34624350.3254630NEUTRON DIFFRACTION0.0225110487395.4
2.4-2.530.3322565.20.3154692NEUTRON DIFFRACTION0.0215119494896.7
2.53-2.690.3282264.60.3144663NEUTRON DIFFRACTION0.0225095488995.9
2.69-2.890.2692434.90.2894676NEUTRON DIFFRACTION0.0175087491996.7
2.89-3.180.30225150.2664734NEUTRON DIFFRACTION0.0195119498597.4
3.18-3.640.26725550.2454798NEUTRON DIFFRACTION0.0175130505398.5
3.64-4.560.282494.90.2454857NEUTRON DIFFRACTION0.0185138510699.4
4.56-14.420.3882585.20.3834681NEUTRON DIFFRACTION0.0245208493994.8
2-2.090.2243055.10.2065676X-RAY DIFFRACTION0.0137780598176.9
2.09-2.20.2123425.30.1866146X-RAY DIFFRACTION0.0117756648883.7
2.2-2.340.193515.10.1766466X-RAY DIFFRACTION0.017784681787.6
2.34-2.520.1993575.10.1726654X-RAY DIFFRACTION0.0117801701189.9
2.52-2.770.1953635.10.1696820X-RAY DIFFRACTION0.017773718392.4
2.77-3.170.1783604.90.1587052X-RAY DIFFRACTION0.0097781741295.3
3.17-40.1453774.90.1317264X-RAY DIFFRACTION0.0077830764197.6
4-29.390.1453985.10.1447400X-RAY DIFFRACTION0.0077940779898.2

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