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- PDB-9o5g: Room-temperature joint X-ray/Neutron structure of Thermus thermop... -

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Basic information

Entry
Database: PDB / ID: 9o5g
TitleRoom-temperature joint X-ray/Neutron structure of Thermus thermophilus SHMT in complex with PLP-Gly external aldimine and 5-methyl-tetrahydrofolate (5MTHF)
ComponentsSerine hydroxymethyltransferase
KeywordsTRANSFERASE / PLP-dependent enzyme / glycine external aldimine / 5-methyl-tetrahydrofolate
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
5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID / DEUTERATED WATER / Chem-PLG / Serine hydroxymethyltransferase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKovalevsky, A. / Drago, V.N. / Phillips, R.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM137008 United States
CitationJournal: Febs J. / Year: 2026
Title: Neutron diffraction reveals protonation states in pyridoxal-5'-phosphate-free and glycine external aldimine-bound serine hydroxymethyltransferase.
Authors: Drago, V.N. / Blakeley, M.P. / Phillips, R.S. / Kovalevsky, A.
History
DepositionApr 10, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2026Provider: 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)90,1469
Polymers88,9002
Non-polymers1,2467
Water7,152397
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9670 Å2
ΔGint-134 kcal/mol
Surface area26420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.917, 83.683, 95.523
Angle α, β, γ (deg.)90.00, 91.64, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Serine hydroxymethyltransferase / SHMT / Serine methylase


Mass: 44449.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: glyA, TthAA11_16450 / Production host: Escherichia coli (E. coli)
References: UniProt: A0AAD1KUU5, glycine hydroxymethyltransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PLG / N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE] / N-PYRIDOXYL-GLYCINE-5-MONOPHOSPHATE


Mass: 306.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N2O7P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-C2F / 5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID


Mass: 459.456 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H25N7O6 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 397 / Source method: isolated from a natural source / Formula: D2O
Has ligand of interestY
Has protein modificationN

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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: 2.65 Å3/Da / Density % sol: 53.55 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 50mM NaOAc, 0.5M Li2SO4, 1.0M Ammonium SO4

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
12931N
22931N
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
NUCLEAR REACTORILL LADI III12.8-3.75
ROTATING ANODERIGAKU MICROMAX-007 HF21.54
Detector
TypeIDDetectorDate
LADI III1IMAGE PLATEApr 24, 2024
DECTRIS EIGER R 4M2PIXELAug 7, 2024
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1LAUELneutron1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
12.81
23.751
31.541
Reflection

Entry-ID: 9O5G / CC1/2: 0.989

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Rmerge(I) obsDiffraction-IDNet I/σ(I)
2.1-50.74099776.65.20.22416.3
1.7-95.510115999.34.20.089221.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Diffraction-ID% possible all
2.1-2.215.50.4952.548900.718162.7
1.7-1.7630.4871.898120.667296.3

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Processing

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

Biso max: 80.06 Å2 / Biso mean: 19.2 Å2 / Biso min: 4 Å2 / 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: 24.8183 Å2 / ksol: 0.590875 e/Å3

Resolution (Å)Refine-IDRfactor RfreeRfactor Rfree errorRfactor RworkNum. reflection RfreeNum. reflection RworkNum. reflection obs% reflection Rfree (%)% reflection obs (%)Diffraction-ID
2.1-36.58NEUTRON DIFFRACTION0.3270.010.292190134539364405.267.51
1.7-29.45X-RAY DIFFRACTION0.1950.0030.181452887395919234.990.22
Refine analyze
Refine-ID#notag 0
NEUTRON DIFFRACTION
FreeObs
Luzzati coordinate error0.420.42
Luzzati d res low-5
Luzzati sigma a-0.75
X-RAY DIFFRACTION
FreeObs
Luzzati coordinate error0.180.16
Luzzati d res low-5
Luzzati sigma a-0.15
Refine funct minimized
Refine-IDType
NEUTRON DIFFRACTIONJoint X-ray/neutron ML
X-RAY DIFFRACTIONJoint X-ray/neutron ML
Refinement stepCycle: LAST / Resolution: 2.1→36.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6220 0 78 397 6695
Refine LS restraints
Refine-IDTypeDev ideal
NEUTRON DIFFRACTIONx_bond_d0.007
NEUTRON DIFFRACTIONx_angle_deg1
NEUTRON DIFFRACTIONx_torsion_deg17.9
NEUTRON DIFFRACTIONx_torsion_impr_deg1.65
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1
X-RAY DIFFRACTIONx_torsion_deg17.9
X-RAY DIFFRACTIONx_torsion_impr_deg1.65
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRefine-IDRfactor Rfree error% reflection obs (%)
2.1-2.20.4311404.60.4442885NEUTRON DIFFRACTION0.03645.1
2.2-2.310.3631414.20.4233215NEUTRON DIFFRACTION0.03149.7
2.31-2.460.3971925.30.3863452NEUTRON DIFFRACTION0.02954.3
2.46-2.650.3792245.70.3853730NEUTRON DIFFRACTION0.02558.8
2.65-2.920.3362315.20.3454247NEUTRON DIFFRACTION0.02266.3
2.92-3.340.3472805.30.3184983NEUTRON DIFFRACTION0.02178.4
3.34-4.20.3043054.90.2855892NEUTRON DIFFRACTION0.01791.1
4.2-36.580.4453885.90.426135NEUTRON DIFFRACTION0.02395.1
1.7-1.780.2314214.70.238473X-RAY DIFFRACTION0.01170.1
1.78-1.870.2234894.80.219630X-RAY DIFFRACTION0.0179.6
1.87-1.990.2134904.40.19510580X-RAY DIFFRACTION0.0187.1
1.99-2.140.1985504.60.18111297X-RAY DIFFRACTION0.00893.2
2.14-2.360.1895774.70.17611649X-RAY DIFFRACTION0.00896
2.36-2.70.1966415.10.17611821X-RAY DIFFRACTION0.00897.8
2.7-3.40.1786815.40.16211915X-RAY DIFFRACTION0.00798.9
3.4-29.450.1646795.30.15312030X-RAY DIFFRACTION0.00698.2

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