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- PDB-8aql: High-resolution crystal structure of human SHMT2 -

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Basic information

Entry
Database: PDB / ID: 8aql
TitleHigh-resolution crystal structure of human SHMT2
ComponentsSerine hydroxymethyltransferase, mitochondrial
KeywordsTRANSFERASE / one-carbon metabolism / tetrahydrofolate / folate cycle / mitochondria
Function / homology
Function and homology information


BRISC complex / L-allo-threonine aldolase activity / regulation of mitochondrial translation / L-serine metabolic process / glycine metabolic process / L-serine biosynthetic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / serine binding ...BRISC complex / L-allo-threonine aldolase activity / regulation of mitochondrial translation / L-serine metabolic process / glycine metabolic process / L-serine biosynthetic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / serine binding / Metabolism of folate and pterines / L-serine catabolic process / regulation of oxidative phosphorylation / tetrahydrofolate metabolic process / response to type I interferon / protein K63-linked deubiquitination / tetrahydrofolate interconversion / regulation of aerobic respiration / cobalt ion binding / mitochondrial nucleoid / RHOG GTPase cycle / folic acid metabolic process / Mitochondrial protein degradation / protein tetramerization / microtubule cytoskeleton / pyridoxal phosphate binding / one-carbon metabolic process / protein homotetramerization / mitochondrial inner membrane / mitochondrial matrix / chromatin binding / positive regulation of cell population proliferation / mitochondrion / zinc ion binding / extracellular exosome / identical protein binding / nucleus / 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
Chem-PLG / Serine hydroxymethyltransferase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.23 Å
AuthorsTran, L.H. / Ruszkowski, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: High-resolution crystal structure of human SHMT2
Authors: Tran, L.H. / Ruszkowski, M.
History
DepositionAug 12, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine hydroxymethyltransferase, mitochondrial
B: Serine hydroxymethyltransferase, mitochondrial
C: Serine hydroxymethyltransferase, mitochondrial
D: Serine hydroxymethyltransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,58916
Polymers210,8674
Non-polymers1,72112
Water25,2571402
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.928, 125.107, 134.568
Angle α, β, γ (deg.)90.00, 93.58, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 52716.855 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SHMT2 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P34897, glycine hydroxymethyltransferase
#2: 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.: 4 / Source method: obtained synthetically / Formula: C10H15N2O7P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1402 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.45 Å3/Da / Density % sol: 49.76 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 9.3
Details: 0.1 M BICINE pH 9.3, 22% v/v PEG Smear Board, 50 mM glycine, raltitrexed (powder was added); 1 uL of this solution supplemented with 50% ethylene glycol was added to the drop with crystals for cryoprotection

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.977 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.23→91.54 Å / Num. obs: 332491 / % possible obs: 59.7 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.027 / Rrim(I) all: 0.069 / Net I/σ(I): 13.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.23-1.346.90.6972.6166270.7430.2830.75313.4
3.99-91.5470.04435.6166200.9980.0180.04899.7

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Processing

Software
NameVersionClassification
XDSdata reduction
PHASERphasing
PHENIX1.20.1-4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QVL

6qvl


Resolution: 1.23→55.15 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.5 / Stereochemistry target values: ML
Details: Hydrogen atoms at riding positions were added for refinement. B factor of non H atoms were refined anisotropically
RfactorNum. reflection% reflectionSelection details
Rfree0.2294 1608 0.48 %RANDOM
Rwork0.1949 ---
obs0.195 332420 59.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.23→55.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14213 0 112 1402 15727
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.011
X-RAY DIFFRACTIONf_angle_d1.134
X-RAY DIFFRACTIONf_dihedral_angle_d13.847
X-RAY DIFFRACTIONf_chiral_restr0.077
X-RAY DIFFRACTIONf_plane_restr0.011
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.23-1.270.2581180.22713819X-RAY DIFFRACTION8
1.27-1.320.2612370.22247643X-RAY DIFFRACTION15
1.32-1.370.2755550.217812627X-RAY DIFFRACTION25
1.37-1.430.2265820.230216538X-RAY DIFFRACTION33
1.43-1.510.2442990.224222176X-RAY DIFFRACTION44
1.51-1.60.22511490.219430163X-RAY DIFFRACTION60
1.6-1.730.23821770.215338551X-RAY DIFFRACTION76
1.73-1.90.28812420.210747640X-RAY DIFFRACTION95
1.9-2.180.22892450.194950417X-RAY DIFFRACTION100
2.18-2.740.22372580.19750440X-RAY DIFFRACTION100
2.74-55.150.21632460.180850798X-RAY DIFFRACTION100

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