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- PDB-10zb: Room-temperature X-ray structure of E53Q mutant of Thermus thermo... -

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Basic information

Entry
Database: PDB / ID: 10zb
TitleRoom-temperature X-ray structure of E53Q mutant of Thermus thermophilus serine hydroxymethyltransferase (TthSHMT) in complex with PLP-L-Ser external aldimine and tetrahydrofolate (THF)
Components(Serine hydroxymethyltransferase) x 2
KeywordsTRANSFERASE / homodimer / pyridoxal-5'-phosphate / one-carbon metabolism / inactive mutant / enzyme-substrate complex
Function / homology
Function and homology information


glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / : / 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
ACETATE ION / Chem-KOU / (6S)-5,6,7,8-TETRAHYDROFOLATE / Serine hydroxymethyltransferase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 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: Rsc Adv / Year: 2026
Title: Mutation of active site glutamate in serine hydroxymethyltransferase allows trapping a reactive intermediate: a combined neutron and X-ray crystallography study
Authors: Drago, V.N. / Phillips, R.S. / Kovalevsky, A.
History
DepositionFeb 12, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 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)90,2538
Polymers89,1262
Non-polymers1,1276
Water7,260403
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9140 Å2
ΔGint-69 kcal/mol
Surface area25840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.859, 83.602, 95.338
Angle α, β, γ (deg.)90.00, 91.69, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Serine hydroxymethyltransferase / SHMT / Serine methylase


Mass: 44677.031 Da / Num. of mol.: 1 / Mutation: E53Q
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: Protein Serine hydroxymethyltransferase / SHMT / Serine methylase


Mass: 44448.914 Da / Num. of mol.: 1
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

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Non-polymers , 5 types, 409 molecules

#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-KOU / (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-serine


Mass: 334.219 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15N2O8P / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-THG / (6S)-5,6,7,8-TETRAHYDROFOLATE


Mass: 445.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H23N7O6 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 403 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 53.24 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 40 mM NaOAc, pH 5.5, 1M ammonium sulfate, 0.5M lithium sulfate

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54186 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Jul 19, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54186 Å / Relative weight: 1
ReflectionResolution: 1.8→95.3 Å / Num. obs: 85253 / % possible obs: 99.6 % / Redundancy: 5 % / CC1/2: 0.971 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.058 / Net I/σ(I): 21
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 4.6 / Num. unique obs: 8531 / CC1/2: 0.87 / Rpim(I) all: 0.171 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
CrysalisProdata reduction
Aimlessdata scaling
CrysalisProdata collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→27.88 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / Phase error: 17.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.185 4252 5 %random
Rwork0.1575 ---
obs0.1589 85110 99.51 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→27.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6235 0 73 403 6711
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096494
X-RAY DIFFRACTIONf_angle_d1.0018812
X-RAY DIFFRACTIONf_dihedral_angle_d8.572930
X-RAY DIFFRACTIONf_chiral_restr0.063964
X-RAY DIFFRACTIONf_plane_restr0.011163
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.23211290.19562674X-RAY DIFFRACTION99
1.82-1.840.24271560.19152683X-RAY DIFFRACTION100
1.84-1.860.22651230.17392709X-RAY DIFFRACTION100
1.86-1.890.2111450.16632680X-RAY DIFFRACTION100
1.89-1.910.19471330.1632704X-RAY DIFFRACTION100
1.91-1.940.20981600.16432692X-RAY DIFFRACTION100
1.94-1.970.21451620.16662692X-RAY DIFFRACTION100
1.97-20.20931290.16662689X-RAY DIFFRACTION100
2-2.030.18631270.16252738X-RAY DIFFRACTION100
2.03-2.060.21411460.15652663X-RAY DIFFRACTION100
2.06-2.10.19651500.16132721X-RAY DIFFRACTION100
2.1-2.130.19391590.16062679X-RAY DIFFRACTION100
2.13-2.180.21031460.16482701X-RAY DIFFRACTION100
2.18-2.220.18811590.15262687X-RAY DIFFRACTION100
2.22-2.270.16281350.15642719X-RAY DIFFRACTION100
2.27-2.320.17771650.15412639X-RAY DIFFRACTION100
2.32-2.380.20621520.16032707X-RAY DIFFRACTION100
2.38-2.440.19611540.16152715X-RAY DIFFRACTION100
2.44-2.510.18621360.16392672X-RAY DIFFRACTION100
2.51-2.60.21071450.16622698X-RAY DIFFRACTION100
2.6-2.690.19811280.17022748X-RAY DIFFRACTION100
2.69-2.80.20041320.16512692X-RAY DIFFRACTION100
2.8-2.920.18071400.15932703X-RAY DIFFRACTION100
2.92-3.080.16871370.15432735X-RAY DIFFRACTION100
3.08-3.270.16991230.15452707X-RAY DIFFRACTION99
3.27-3.520.15591260.15152735X-RAY DIFFRACTION99
3.52-3.870.15041250.12842671X-RAY DIFFRACTION98
3.87-4.430.13731450.12852685X-RAY DIFFRACTION98
4.43-5.580.17441230.14182718X-RAY DIFFRACTION98
5.58-27.880.19071620.18952602X-RAY DIFFRACTION94

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