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- PDB-6m5o: Co-crystal structure of human serine hydroxymethyltransferase 2 i... -

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Basic information

Entry
Database: PDB / ID: 6m5o
TitleCo-crystal structure of human serine hydroxymethyltransferase 2 in complex with Pyridoxal 5'-phosphate (PLP) and glycodeoxycholic acid
ComponentsSerine hydroxymethyltransferase, mitochondrial
KeywordsTRANSFERASE / Inhibitor / Complex
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
GLYCINE / Serine hydroxymethyltransferase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.30000663987 Å
AuthorsOta, T. / Senoo, A. / Ito, S. / Ueno, G. / Nagatoishi, S. / Tsumoto, K. / Sando, S.
CitationJournal: Iscience / Year: 2021
Title: Structural basis for selective inhibition of human serine hydroxymethyltransferase by secondary bile acid conjugate.
Authors: Ota, T. / Senoo, A. / Shirakawa, M. / Nonaka, H. / Saito, Y. / Ito, S. / Ueno, G. / Nagatoishi, S. / Tsumoto, K. / Sando, S.
History
DepositionMar 11, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Database references / Structure summary / Category: audit_author / citation / Item: _citation.title
Revision 1.2Feb 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)113,6216
Polymers112,6862
Non-polymers9354
Water8,827490
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, SEC-MALS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10630 Å2
ΔGint-44 kcal/mol
Surface area31960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.840, 159.840, 211.210
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Components on special symmetry positions
IDModelComponents
11A-1004-

HOH

21A-1013-

HOH

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Components

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


Mass: 56342.805 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
#2: Chemical ChemComp-DXC / (3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID / DEOXYCHOLIC ACID


Mass: 392.572 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H40O4 / Comment: detergent*YM
#3: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 490 / 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: 3.43 Å3/Da / Density % sol: 64.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris hydrochloride pH 8.5, 8% (w/v) polyethylene glycol 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: May 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→49.3564705048 Å / Num. obs: 70999 / % possible obs: 100 % / Redundancy: 22.25 % / Rmerge(I) obs: 0.316 / Rrim(I) all: 0.324 / Net I/σ(I): 12.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRrim(I) all% possible all
2.3-2.3822.481.8782.31574631.921100
2.38-2.4822.461.5292.81565671.564100
2.48-2.5922.491.3573.41571831.28599.97
2.59-2.7322.480.9464.41574200.967100
2.73-2.922.450.7215.71579970.737100
2.9-3.1222.430.4888.11578980.499100
3.12-3.4422.390.33311.31585360.34100
3.44-3.9322.280.18818.81585170.192100
3.93-4.9522.060.11528.21590760.118100

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.11refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PVF

4pvf


Resolution: 2.30000663987→49.3564705048 Å / SU ML: 0.303512515499 / Cross valid method: FREE R-VALUE / σ(F): 1.35660850073 / Phase error: 26.6768656715
RfactorNum. reflection% reflection
Rfree0.255867853927 3514 4.95152744899 %
Rwork0.201122980691 --
obs0.203792694894 70968 99.9549295775 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 42.9272779355 Å2
Refinement stepCycle: LAST / Resolution: 2.30000663987→49.3564705048 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7306 0 0 490 7796
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00698243060437460
X-RAY DIFFRACTIONf_angle_d0.96158276486810112
X-RAY DIFFRACTIONf_chiral_restr0.04946987695991118
X-RAY DIFFRACTIONf_plane_restr0.005647282300511318
X-RAY DIFFRACTIONf_dihedral_angle_d16.31486890674536
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.30000663987-2.33150.3365313230651300.2889654542172647X-RAY DIFFRACTION99.8920863309
2.3315-2.36480.3294859096571280.2816244648712690X-RAY DIFFRACTION99.9645264278
2.3648-2.40010.3391458176061530.2791695642642617X-RAY DIFFRACTION99.8558038933
2.4001-2.43760.3426689813281400.2705121154572654X-RAY DIFFRACTION99.9642218247
2.4376-2.47760.3278222562861410.2628804607092663X-RAY DIFFRACTION99.9287241625
2.4776-2.52030.2795488567361400.2628668378832656X-RAY DIFFRACTION99.9285203717
2.5203-2.56610.3111160259861340.2524606441872652X-RAY DIFFRACTION100
2.5661-2.61550.3114997193421360.2509942367032671X-RAY DIFFRACTION99.9643874644
2.6155-2.66890.3145391741641550.2542311706642663X-RAY DIFFRACTION99.9645264278
2.6689-2.72690.3294493792921320.2496643145422651X-RAY DIFFRACTION99.9640804598
2.7269-2.79030.3337664122861570.250343777622657X-RAY DIFFRACTION100
2.7903-2.86010.3406948974651360.2414196529152672X-RAY DIFFRACTION99.8932764141
2.8601-2.93740.3206936177091610.2299434102652651X-RAY DIFFRACTION99.8934280639
2.9374-3.02380.3058058914251300.236319800612687X-RAY DIFFRACTION99.9290528556
3.0238-3.12140.2927685441421430.2330368802362671X-RAY DIFFRACTION99.9289772727
3.1214-3.2330.2758646369861280.2217630777972705X-RAY DIFFRACTION100
3.233-3.36240.2785347097161340.2148770822922686X-RAY DIFFRACTION100
3.3624-3.51540.2557194148851400.1933070009172709X-RAY DIFFRACTION99.9649122807
3.5154-3.70070.2294568627821370.1830997056022706X-RAY DIFFRACTION100
3.7007-3.93240.1908296026231340.1638988158912717X-RAY DIFFRACTION100
3.9324-4.23590.2060526262061500.1517479408362726X-RAY DIFFRACTION100
4.2359-4.66190.179851888861250.1423930270652757X-RAY DIFFRACTION100
4.6619-5.33580.2033729827811570.1436244053432761X-RAY DIFFRACTION100
5.3358-6.71980.1984305948311500.1682302004442798X-RAY DIFFRACTION100
6.7198-49.35647050480.187596896791430.1591674289732987X-RAY DIFFRACTION99.8405103668
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.111370032838-0.01880968570650.01433268446440.00148588179970.02615215844890.0641762894472-0.0831900875805-0.0431152751304-0.0123540604788-0.0632863943738-0.0740831134324-0.0538731556649-0.0580774140838-0.205495350744-0.190810723027-0.02301298671340.172224452267-0.01420145304860.3220548287020.04461645774250.19531252970425.295923196461.3702195564-3.81993269076
20.0368984395979-0.02102054045340.02712306064540.03546629924030.01108682708010.0847039869348-0.0233966324914-0.0839159758603-0.09814211971770.05173640110830.00710065857929-0.03455501721030.0238565570051-0.123467680404-0.0161795296631-0.01252223277730.1218325905-0.01631191617430.211548139092-0.01029735050750.22331459441429.007135712352.19013080322.17289237874
30.007687220495580.01335095297850.0160013579540.06931583628880.07436307898580.1058767051640.01444817056920.0673076133497-0.0955237727355-0.08520621224630.01448632660090.0107569360709-0.1299650904860.133379929225-0.003250488647660.116190731806-0.0257407921315-0.0004806905999190.2668756042160.01906853662310.22678144228746.616039294162.7794155802-19.9663906257
40.0209394170405-0.02844104370770.0218426250662-0.006709341007560.004159442499840.0439063948146-0.234380435891-0.1945989461170.196519692559-0.0448236835979-0.09536661773350.11560516609-0.313552609675-0.440848940373-0.622379815430.06095509514450.772745912406-0.2074172400360.40441574712-0.2235491981660.29965984045212.540197508776.4464089769-5.15315051975
50.072181614719-0.05305147697110.0119914593280.0534980359333-0.04800744246530.0634778724725-0.059144519486-0.06696253824950.06853270290030.00264470097224-0.1599337355570.116698331426-0.127131198793-0.384484455245-0.4220783598110.03819598222140.51186040854-0.2677771680890.793821441067-0.2562889469620.300749244744-1.6827759097871.1261506998-7.60187187505
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 43 through 216 )
2X-RAY DIFFRACTION2chain 'A' and (resid 217 through 367 )
3X-RAY DIFFRACTION3chain 'A' and (resid 368 through 504 )
4X-RAY DIFFRACTION4chain 'B' and (resid 43 through 277 )
5X-RAY DIFFRACTION5chain 'B' and (resid 278 through 504 )

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