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

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Basic information

Entry
Database: PDB / ID: 8suj
TitleJoint X-ray/neutron structure of Thermus thermophilus serine hydroxymethyltransferase (TthSHMT) in internal aldimine state
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 hydroxymethyltransferase
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / NUCLEAR REACTOR / 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
Citation
Journal: 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.
#1: Journal: Acta Cryst. / Year: 2009
Title: Generalized X-ray and neutron crystallographic analysis: more accurate and complete structures for biological macromolecules
Authors: Adams, P.D. / Mustyakimov, M. / Afonine, P.V. / Langan, P.
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)89,5484
Polymers89,3562
Non-polymers1922
Water7,728429
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8030 Å2
ΔGint-96 kcal/mol
Surface area26230 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
#3: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 429 / 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)
NUCLEAR REACTORORNL High Flux Isotope Reactor CG4D12.8-4.5
ROTATING ANODERIGAKU MICROMAX-007 HF21.54
Detector
TypeIDDetectorDateDetails
MAATEL IMAGINE1IMAGE PLATEMar 29, 2022elliptical mirrors
DECTRIS EIGER R 4M2PIXELMay 23, 2022Osmic VariMax
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1NONELAUELneutron1
2NONESINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
12.81
24.51
31.541
Reflection

Entry-ID: 8SUJ

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)CC1/2Rmerge(I) obsRpim(I) allDiffraction-IDNet I/σ(I)
2.3-47.783258685.44.10.9430.1610.0814.3
2-95.546236499.95.40.9930.0910.044217.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allDiffraction-ID% possible all
2.3-2.423.80.2812.944900.6370.145174.7
2-2.075.20.3643.962260.8820.1177299.6

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Processing

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

Biso max: 78.28 Å2 / Biso mean: 18.35 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: 18.9252 Å2 / ksol: 0.581345 e/Å3

Resolution (Å)Refine-IDRfactor RfreeRfactor Rfree errorRfactor RworkNum. reflection RfreeNum. reflection RworkNum. reflection obs% reflection obs (%)Diffraction-ID
2.3-40NEUTRON DIFFRACTION0.2390.0080.211553310463106575.51
2-40X-RAY DIFFRACTION0.1770.0030.1642954552475890294.42
Refine analyze
Refine-ID#notag 0
NEUTRON DIFFRACTION
FreeObs
Luzzati coordinate error0.390.39
Luzzati d res low-5
Luzzati sigma a0.440.46
Luzzati d res high-2.3
X-RAY DIFFRACTION
FreeObs
Luzzati coordinate error0.180.17
Luzzati d res low-5
Luzzati sigma a0.150.15
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 10 429 6689
Refine LS restraints
Refine-IDTypeDev ideal
NEUTRON DIFFRACTIONx_bond_d0.008
NEUTRON DIFFRACTIONx_angle_deg1
NEUTRON DIFFRACTIONx_torsion_deg18
NEUTRON DIFFRACTIONx_torsion_impr_deg0.79
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1
X-RAY DIFFRACTIONx_torsion_deg18
X-RAY DIFFRACTIONx_torsion_impr_deg0.79
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRefine-IDRfactor Rfree error% reflection obs (%)
2.3-2.40.3534.30.3623150NEUTRON DIFFRACTION0.0364.1
2.4-2.530.3317350.3513285NEUTRON DIFFRACTION0.02567.3
2.53-2.690.36721460.3543350NEUTRON DIFFRACTION0.02569.7
2.69-2.90.3091965.10.3353614NEUTRON DIFFRACTION0.02274.5
2.9-3.190.3332335.60.3123951NEUTRON DIFFRACTION0.02281.3
3.19-3.650.2652164.70.2734374NEUTRON DIFFRACTION0.01889.1
3.65-4.60.2782645.50.2634578NEUTRON DIFFRACTION0.01794.2
4.6-38.190.4012294.60.4024744NEUTRON DIFFRACTION0.02794.8
2-2.090.1932914.50.1946235X-RAY DIFFRACTION0.01183.9
2.09-2.20.1973184.60.1816533X-RAY DIFFRACTION0.01188.4
2.2-2.340.173434.80.1716739X-RAY DIFFRACTION0.00991
2.34-2.520.1833524.80.1716925X-RAY DIFFRACTION0.0193.3
2.52-2.770.1643915.30.176962X-RAY DIFFRACTION0.00894.6
2.77-3.170.1613995.30.1587114X-RAY DIFFRACTION0.00896.6
3.17-40.1363704.80.1317295X-RAY DIFFRACTION0.00797.9
4-29.740.1373864.90.1427444X-RAY DIFFRACTION0.00798.6

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