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- PDB-8xnd: Crystal structure of serine hydroxymethyltransferase 1 -

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Basic information

Entry
Database: PDB / ID: 8xnd
TitleCrystal structure of serine hydroxymethyltransferase 1
ComponentsSerine hydroxymethyltransferase, cytosolic
KeywordsTRANSFERASE / methyltransferase
Function / homology
Function and homology information


cellular response to tetrahydrofolate / Carnitine synthesis / carnitine biosynthetic process / purine nucleobase biosynthetic process / serine binding / L-serine catabolic process / glycine metabolic process / L-serine metabolic process / aldehyde-lyase activity / glycine hydroxymethyltransferase ...cellular response to tetrahydrofolate / Carnitine synthesis / carnitine biosynthetic process / purine nucleobase biosynthetic process / serine binding / L-serine catabolic process / glycine metabolic process / L-serine metabolic process / aldehyde-lyase activity / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from L-serine / Metabolism of folate and pterines / tetrahydrofolate metabolic process / tetrahydrofolate interconversion / dTMP biosynthetic process / small molecule binding / folic acid metabolic process / mRNA regulatory element binding translation repressor activity / cellular response to leukemia inhibitory factor / mRNA 5'-UTR binding / pyridoxal phosphate binding / protein homotetramerization / negative regulation of translation / protein homodimerization activity / mitochondrion / extracellular exosome / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
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
PYRIDOXAL-5'-PHOSPHATE / Serine hydroxymethyltransferase, cytosolic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.45 Å
AuthorsFan, S. / Wei, X. / Lv, R. / Wang, C. / Tang, M. / Jin, Y. / Yang, Z.
Funding support1items
OrganizationGrant numberCountry
Other government2018YFA0901800
CitationJournal: To Be Published
Title: Crystal structure of serine hydroxymethyltransferase 1
Authors: Fan, S. / Wei, X. / Lv, R. / Wang, C. / Tang, M. / Jin, Y. / Yang, Z.
History
DepositionDec 29, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 2, 2025Provider: 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, cytosolic
B: Serine hydroxymethyltransferase, cytosolic
C: Serine hydroxymethyltransferase, cytosolic
D: Serine hydroxymethyltransferase, cytosolic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,8158
Polymers206,8274
Non-polymers9894
Water00
1
A: Serine hydroxymethyltransferase, cytosolic
D: Serine hydroxymethyltransferase, cytosolic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,9084
Polymers103,4132
Non-polymers4942
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10540 Å2
ΔGint-68 kcal/mol
Surface area32750 Å2
MethodPISA
2
B: Serine hydroxymethyltransferase, cytosolic
C: Serine hydroxymethyltransferase, cytosolic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,9084
Polymers103,4132
Non-polymers4942
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10720 Å2
ΔGint-61 kcal/mol
Surface area32990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.540, 151.540, 234.970
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
Serine hydroxymethyltransferase, cytosolic / SHMT / Glycine hydroxymethyltransferase / Serine methylase


Mass: 51706.715 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SHMT1 / Production host: Escherichia coli (E. coli)
References: UniProt: P34896, glycine hydroxymethyltransferase
#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P
Has ligand of interestN
Has protein modificationN

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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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Sodium HEPES pH 7.5,30 %(v/v) PEG 300

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.18057 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18057 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.228
11K, H, -L20.231
11-h,-k,l30.24
11-K, -H, -L40.301
ReflectionResolution: 3.45→48.53 Å / Num. obs: 79382 / % possible obs: 99.9 % / Redundancy: 5.3 % / CC1/2: 0.995 / Rmerge(I) obs: 0.161 / Net I/σ(I): 10.4
Reflection shellResolution: 3.45→3.52 Å / Num. unique obs: 4531 / CC1/2: 0.787

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.45→48.53 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / SU B: 6.096 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19205 4049 5.1 %RANDOM
Rwork0.153 ---
obs0.15499 75288 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 90.799 Å2
Baniso -1Baniso -2Baniso -3
1-46.38 Å20 Å20 Å2
2--46.38 Å20 Å2
3----92.77 Å2
Refinement stepCycle: 1 / Resolution: 3.45→48.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14528 0 60 0 14588
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01214885
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.6931.83320142
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.62851884
X-RAY DIFFRACTIONr_dihedral_angle_2_deg15.204592
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.804102532
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1670.22232
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211232
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it15.3439.0887548
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it21.37416.1979428
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it17.2568.9747337
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined27.293109.2267195
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.45→3.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 334 -
Rwork0.192 5484 -
obs--99.78 %

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