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- PDB-6qvl: Human SHMT2 in complex with pemetrexed -

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Basic information

Entry
Database: PDB / ID: 6qvl
TitleHuman SHMT2 in complex with pemetrexed
ComponentsSerine hydroxymethyltransferase, mitochondrial
KeywordsTRANSFERASE
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 / Metabolism of folate and pterines ...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 / Metabolism of folate and pterines / regulation of oxidative phosphorylation / tetrahydrofolate metabolic process / response to type I interferon / protein K63-linked deubiquitination / tetrahydrofolate interconversion / regulation of aerobic respiration / amino acid binding / mitochondrial nucleoid / RHOG GTPase cycle / 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 / 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-4DW / DI(HYDROXYETHYL)ETHER / PYRIDOXAL-5'-PHOSPHATE / Serine hydroxymethyltransferase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsScaletti, E. / Jemth, A.S. / Helleday, T. / Stenmark, P.
CitationJournal: Febs Lett. / Year: 2019
Title: Structural basis of inhibition of the human serine hydroxymethyltransferase SHMT2 by antifolate drugs.
Authors: Scaletti, E. / Jemth, A.S. / Helleday, T. / Stenmark, P.
History
DepositionMar 3, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2019Provider: 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, mitochondrial
B: Serine hydroxymethyltransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,47810
Polymers112,1362
Non-polymers1,3428
Water7,728429
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11500 Å2
ΔGint-44 kcal/mol
Surface area31400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.208, 160.208, 209.442
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 56067.879 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SHMT2 / Production host: Escherichia coli (E. coli)
References: UniProt: P34897, glycine hydroxymethyltransferase

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Non-polymers , 6 types, 437 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#6: Chemical ChemComp-4DW / N-{4-[2-(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)ethyl]benzoyl}-L-glutamic acid / pemetrexed


Mass: 425.395 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H19N5O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, chemotherapy*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 429 / Source method: isolated from a natural source / Formula: H2O

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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: 3.46 Å3/Da / Density % sol: 64.45 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 0.2 M LiCl2, 0.1 M MES pH 6.0, 20 % PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.07 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 2.28→52.7 Å / Num. obs: 1458540 / % possible obs: 99.8 % / Redundancy: 12.3 % / Net I/σ(I): 2.7
Reflection shellResolution: 2.28→52.7 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.28→52.63 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.908 / SU B: 7.342 / SU ML: 0.167 / Cross valid method: THROUGHOUT / ESU R: 0.219 / ESU R Free: 0.2 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25908 3602 5 %RANDOM
Rwork0.21185 ---
obs0.2142 69006 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 40.73 Å2
Baniso -1Baniso -2Baniso -3
1-0.98 Å20.49 Å20 Å2
2--0.98 Å20 Å2
3----3.19 Å2
Refinement stepCycle: 1 / Resolution: 2.28→52.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7087 0 87 429 7603
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0197357
X-RAY DIFFRACTIONr_bond_other_d0.0020.026892
X-RAY DIFFRACTIONr_angle_refined_deg1.3961.9779951
X-RAY DIFFRACTIONr_angle_other_deg0.952.99715925
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5835911
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.3722.77343
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.699151236
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.891572
X-RAY DIFFRACTIONr_chiral_restr0.0740.21087
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218237
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021558
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_it2.0023.9863644
X-RAY DIFFRACTIONr_mcbond_other2.0023.9863643
X-RAY DIFFRACTIONr_mcangle_it3.3345.9684555
X-RAY DIFFRACTIONr_mcangle_other3.3345.9684556
X-RAY DIFFRACTIONr_scbond_it1.8984.2563712
X-RAY DIFFRACTIONr_scbond_other1.8984.2573713
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.36.2695397
X-RAY DIFFRACTIONr_long_range_B_refined6.26647.0588319
X-RAY DIFFRACTIONr_long_range_B_other6.26547.0588320
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.279→2.338 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 262 -
Rwork0.33 4999 -
obs--99.83 %

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