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- PDB-6m5w: Co-crystal structure of human serine hydroxymethyltransferase 1 i... -

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Basic information

Entry
Database: PDB / ID: 6m5w
TitleCo-crystal structure of human serine hydroxymethyltransferase 1 in complex with Pyridoxal 5'-phosphate (PLP) and glycodeoxycholic acid
ComponentsSerine hydroxymethyltransferase, cytosolic
KeywordsTRANSFERASE / Inhibitor / Complex
Function / homology
Function and homology information


cellular response to tetrahydrofolate / Carnitine synthesis / purine nucleobase biosynthetic process / L-serine metabolic process / glycine metabolic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / serine binding / Metabolism of folate and pterines ...cellular response to tetrahydrofolate / Carnitine synthesis / purine nucleobase biosynthetic process / L-serine metabolic process / glycine metabolic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / serine binding / Metabolism of folate and pterines / L-serine catabolic process / tetrahydrofolate metabolic process / tetrahydrofolate interconversion / dTMP biosynthetic process / cobalt ion binding / folic acid metabolic process / small molecule binding / 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 / zinc ion binding / extracellular exosome / nucleoplasm / identical protein binding / cytoplasm / 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
GLYCINE / PYRIDOXAL-5'-PHOSPHATE / Serine hydroxymethyltransferase, cytosolic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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

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Assembly

Deposited unit
A: Serine hydroxymethyltransferase, cytosolic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0394
Polymers55,3241
Non-polymers7153
Water00
1
A: Serine hydroxymethyltransferase, cytosolic
hetero molecules

A: Serine hydroxymethyltransferase, cytosolic
hetero molecules

A: Serine hydroxymethyltransferase, cytosolic
hetero molecules

A: Serine hydroxymethyltransferase, cytosolic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,15516
Polymers221,2954
Non-polymers2,85912
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
crystal symmetry operation7_556y,x,-z+5/31
crystal symmetry operation10_666-y+1,-x+1,-z+5/31
Unit cell
Length a, b, c (Å)152.749, 152.749, 235.933
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/3
#3: y,-x+y,z+2/3
#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
#9: y,x,-z+2/3
#10: -y,-x,-z+2/3
#11: -x+y,y,-z
#12: x,x-y,-z+1/3

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Components

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


Mass: 55323.867 Da / Num. of mol.: 1
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.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DXC / (3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID / DEOXYCHOLIC ACID


Mass: 392.572 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H40O4 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM
#4: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
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: 7.1 Å3/Da / Density % sol: 82.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M potassium chloride, 0.05 M HEPES pH 7.5, and 35% (v/v) pentaerythritol propoxylate (5/4 PO/OH)

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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 MX225-HS / Detector: CCD / Date: Apr 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→46.68 Å / Num. obs: 55751 / % possible obs: 99.9 % / Redundancy: 11.826 % / Biso Wilson estimate: 71.594 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.526 / Rrim(I) all: 0.55 / Χ2: 0.726 / Net I/σ(I): 7.31 / Num. measured all: 659305
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.1-3.2911.7374.1570.91105213897489640.5864.34599.9
3.29-3.5211.8242.5571.57100266848284800.7762.672100
3.52-3.811.8461.4632.7892884784378410.911.529100
3.8-4.1611.850.7875.0386032726072600.9710.822100
4.16-4.6411.8680.5037.2377934656865670.9920.526100
4.64-5.3511.8650.3769.5368459577157700.9890.393100
5.35-6.5411.8870.34910.0858377491349110.9910.365100
6.54-9.1611.8340.13122.3744957380137990.9980.13799.9
9.16-46.6811.6640.05642.1325183217721590.9990.05999.2

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Processing

Software
NameVersionClassification
PHENIX1.11refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BJ4

1bj4


Resolution: 3.1→46.68 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2329 1075 5.03 %
Rwork0.1936 20304 -
obs0.1956 21379 71.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 153.76 Å2 / Biso mean: 33.0796 Å2 / Biso min: 6.41 Å2
Refinement stepCycle: final / Resolution: 3.1→46.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3616 0 47 0 3663
Biso mean--41.83 --
Num. residues----470
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1-3.240.3609130.27742122256
3.25-3.420.2759380.259172276021
3.42-3.630.2682870.23061554164144
3.63-3.910.26761680.2243262343093
3.91-4.30.2381560.19635663722100
4.3-4.930.21691780.173335973775100
4.93-6.20.24332070.190835883795100
6.2-46.680.19852280.172138034031100

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