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- PDB-9bpe: Joint X-ray/neutron structure of Thermus thermophilus serine hydr... -

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Basic information

Entry
Database: PDB / ID: 9bpe
TitleJoint X-ray/neutron structure of Thermus thermophilus serine hydroxymethyltransferase (TthSHMT) in internal aldimine state and folinic acid bound
ComponentsSerine hydroxymethyltransferase
KeywordsTRANSFERASE / PYRIDOXAL 5'-PHOSPHATE / PLP / FOLD TYPE 1 / ONE CARBON METABOLISM
Function / homology
Function and homology information


serine binding / L-serine catabolic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / 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
ACETATE ION / DEUTERATED WATER / Chem-FFO / 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 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 7, 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)89,3825
Polymers88,7532
Non-polymers6293
Water7,873437
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9140 Å2
ΔGint-78 kcal/mol
Surface area25940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.764, 83.478, 95.558
Angle α, β, γ (deg.)90.00, 91.52, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Serine hydroxymethyltransferase / SHMT / Serine methylase


Mass: 44376.684 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.: 1 / Source method: obtained synthetically / Formula: SO4
#3: 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
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 437 / 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: 2.64 Å3/Da / Density % sol: 53.46 %
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, soaked in 40 mM NaOAc pH 5.5, 15% PEG 4000, and 10 mM folinic acid

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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 MANDI12.0-4.16
ROTATING ANODERIGAKU MICROMAX-007 HF21.5406
Detector
TypeIDDetectorDateDetails
ORNL ANGER CAMERA1AREA DETECTORFeb 21, 2023
DECTRIS EIGER R 4M2PIXELJan 3, 2023Osmic Varimax
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1NONELAUELneutron1
2MSINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
121
24.161
31.54061
Reflection

Entry-ID: 9BPE

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)CC1/2Rmerge(I) obsRpim(I) allDiffraction-IDNet I/σ(I)
2.3-14.513836292.54.10.9110.2160.10917.3
2-95.56237599.93.70.9870.1240.07429.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allDiffraction-ID% possible all
2.3-2.373.70.2663.233070.4370.141180.1
2-2.073.60.4622.262070.730.279299.3

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Processing

Refinement

Biso max: 116.14 Å2 / Biso min: 4 Å2 / Cross valid method: FREE R-VALUE / Method to determine structure: MOLECULAR REPLACEMENT / Stereochemistry target values: Joint X-ray/neutron ML / Solvent model: CNS bulk solvent model used / Bsol: 31.8133 Å2 / ksol: 0.646537 e/Å3

Resolution (Å)Refine-IDRfactor RfreeRfactor RworkNum. reflection RfreeNum. reflection RworkNum. reflection obs% reflection Rfree (%)% reflection obs (%)Diffraction-IDσ(F)Biso mean (Å2)Rfactor Rfree error
2.3-14.51NEUTRON DIFFRACTION0.2390.21219103616438074592.512.5
2-40X-RAY DIFFRACTION0.1870.162273853093558314.989.4220.20.003
Refine analyze
Refine-ID#notag 0
NEUTRON DIFFRACTION
FreeObs
Luzzati coordinate error0.370.36
Luzzati d res low-5
Luzzati sigma a0.470.44
Luzzati d res high-2.3
X-RAY DIFFRACTION
FreeObs
Luzzati coordinate error0.20.18
Luzzati d res low-5
Luzzati sigma a0.180.17
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→14.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6243 0 43 437 6723
Refine LS restraints
Refine-IDTypeDev ideal
NEUTRON DIFFRACTIONx_bond_d0.007
NEUTRON DIFFRACTIONx_angle_deg1
NEUTRON DIFFRACTIONx_torsion_deg17.2
NEUTRON DIFFRACTIONx_torsion_impr_deg0.78
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1
X-RAY DIFFRACTIONx_torsion_deg17.2
X-RAY DIFFRACTIONx_torsion_impr_deg0.78
LS refinement shellResolution: 2.3→2.32 Å /
RfactorNum. reflection
Rwork0.299 754

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