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- PDB-7x5n: Crystal structure of E. faecium SHMT in complex with (+)-SHIN-1 a... -

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Basic information

Entry
Database: PDB / ID: 7x5n
TitleCrystal structure of E. faecium SHMT in complex with (+)-SHIN-1 and PLP-Ser
ComponentsSerine hydroxymethyltransferase
KeywordsTRANSFERASE / E. faecium / Serine hydroxymethyltransferase / 1C metabolism
Function / homology
Function and homology information


glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / serine binding / L-serine catabolic process / tetrahydrofolate interconversion / cobalt ion binding / folic acid metabolic process / methyltransferase activity / pyridoxal phosphate binding ...glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / serine binding / L-serine catabolic process / tetrahydrofolate interconversion / cobalt ion binding / folic acid metabolic process / methyltransferase activity / pyridoxal phosphate binding / methylation / zinc ion binding / 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
Chem-5M5 / Chem-PLS / Serine hydroxymethyltransferase
Similarity search - Component
Biological speciesEnterococcus faecium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsHasegawa, K. / Hayashi, H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Commun Biol / Year: 2022
Title: Serine hydroxymethyltransferase as a potential target of antibacterial agents acting synergistically with one-carbon metabolism-related inhibitors.
Authors: Makino, Y. / Oe, C. / Iwama, K. / Suzuki, S. / Nishiyama, A. / Hasegawa, K. / Okuda, H. / Hirata, K. / Ueno, M. / Kawaji, K. / Sasano, M. / Usui, E. / Hosaka, T. / Yabuki, Y. / Shirouzu, M. ...Authors: Makino, Y. / Oe, C. / Iwama, K. / Suzuki, S. / Nishiyama, A. / Hasegawa, K. / Okuda, H. / Hirata, K. / Ueno, M. / Kawaji, K. / Sasano, M. / Usui, E. / Hosaka, T. / Yabuki, Y. / Shirouzu, M. / Katsumi, M. / Murayama, K. / Hayashi, H. / Kodama, E.N.
History
DepositionMar 5, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine hydroxymethyltransferase
B: Serine hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,4836
Polymers90,0102
Non-polymers1,4734
Water9,638535
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7200 Å2
ΔGint-49 kcal/mol
Surface area27560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.350, 119.350, 162.588
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Serine hydroxymethyltransferase / SHMT / Serine methylase


Mass: 45005.035 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecium (bacteria)
Gene: glyA, glyA_1, B1P95_02920, BU183_09275, BU187_13395, BU190_13075, BU192_03790, BXT96_08900, CQR37_06830, CUM68_02790, CUN04_11625, CUS10_03200, CWC53_10155, DKP91_07450, DTPHA_1400422, DTPHA_ ...Gene: glyA, glyA_1, B1P95_02920, BU183_09275, BU187_13395, BU190_13075, BU192_03790, BXT96_08900, CQR37_06830, CUM68_02790, CUN04_11625, CUS10_03200, CWC53_10155, DKP91_07450, DTPHA_1400422, DTPHA_600996, EB12_01905, EfmAA708_21800, F6440_11360, GBM44_11330, GBM73_12625, GJ652_13105, SAMEA3893517_00378
Production host: Escherichia coli (E. coli)
References: UniProt: A0A133CK16, glycine hydroxymethyltransferase
#2: Chemical ChemComp-5M5 / (4R)-6-azanyl-4-[3-(hydroxymethyl)-5-phenyl-phenyl]-3-methyl-4-propan-2-yl-1H-pyrano[2,3-c]pyrazole-5-carbonitrile


Mass: 400.473 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H24N4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PLS / [3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-SERINE / PYRIDOXYL-SERINE-5-MONOPHOSPHATE


Mass: 336.235 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H17N2O8P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 535 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Sequence detailsresidue 1 is VAL according to NCBI accession WP_153841961.1

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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: 3.22 Å3/Da / Density % sol: 61.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 0.1M HEPES pH 7.5, 1.4M Sodium citrate tribasic dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→49.35 Å / Num. obs: 92734 / % possible obs: 99.94 % / Redundancy: 26.8 % / Biso Wilson estimate: 35.59 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.05079 / Rrim(I) all: 0.2614 / Net I/σ(I): 14.3
Reflection shellResolution: 1.9→1.968 Å / Redundancy: 27.8 % / Mean I/σ(I) obs: 1 / Num. unique obs: 9141 / CC1/2: 0.652 / Rpim(I) all: 0.6137 / Rrim(I) all: 3.249 / % possible all: 99.95

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Processing

Software
NameVersionClassification
BSSdata collection
XDSdata reduction
PHENIXphasing
Cootmodel building
PHENIX1.19.2refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.9→49.35 Å / SU ML: 0.2723 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.8558
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1974 3402 3.67 %
Rwork0.1743 89288 -
obs0.1752 92690 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.7 Å2
Refinement stepCycle: LAST / Resolution: 1.9→49.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6241 0 104 535 6880
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00626500
X-RAY DIFFRACTIONf_angle_d0.99068830
X-RAY DIFFRACTIONf_chiral_restr0.0528996
X-RAY DIFFRACTIONf_plane_restr0.00561146
X-RAY DIFFRACTIONf_dihedral_angle_d19.3822372
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.930.43771410.39013680X-RAY DIFFRACTION99.95
1.93-1.960.38051380.35413669X-RAY DIFFRACTION99.92
1.96-1.990.29011370.29683662X-RAY DIFFRACTION99.97
1.99-2.020.24731460.25113671X-RAY DIFFRACTION99.95
2.02-2.050.2971350.23163653X-RAY DIFFRACTION99.84
2.05-2.090.23861410.22383686X-RAY DIFFRACTION99.97
2.09-2.130.24641410.21743663X-RAY DIFFRACTION99.95
2.13-2.170.24311410.21673682X-RAY DIFFRACTION99.97
2.17-2.220.23481400.20613687X-RAY DIFFRACTION99.84
2.22-2.270.29081430.2073682X-RAY DIFFRACTION99.92
2.27-2.330.21861370.19333658X-RAY DIFFRACTION99.92
2.33-2.390.23281380.19683710X-RAY DIFFRACTION100
2.39-2.460.22681410.19083700X-RAY DIFFRACTION99.97
2.46-2.540.23731430.19223694X-RAY DIFFRACTION99.92
2.54-2.630.25041390.18473711X-RAY DIFFRACTION100
2.63-2.740.2181410.18433706X-RAY DIFFRACTION100
2.74-2.860.20641470.19093713X-RAY DIFFRACTION99.97
2.86-3.020.22851390.19263732X-RAY DIFFRACTION99.97
3.02-3.20.2261410.19813741X-RAY DIFFRACTION99.95
3.2-3.450.17321450.17513739X-RAY DIFFRACTION99.97
3.45-3.80.18031430.15263778X-RAY DIFFRACTION100
3.8-4.350.14971450.133788X-RAY DIFFRACTION99.97
4.35-5.480.14571460.1323853X-RAY DIFFRACTION100
5.48-49.350.15761540.14374030X-RAY DIFFRACTION99.9

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