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- PDB-7x5o: Crystal structure of E. faecium SHMT in complex with Me-THF and P... -

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Basic information

Entry
Database: PDB / ID: 7x5o
TitleCrystal structure of E. faecium SHMT in complex with Me-THF and PLP-Gly
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 / tetrahydrofolate interconversion / methyltransferase activity / pyridoxal phosphate binding / methylation / 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-PLG / Chem-THH / Serine hydroxymethyltransferase
Similarity search - Component
Biological speciesEnterococcus faecium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 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 1.1Nov 29, 2023Group: 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
B: Serine hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,0017
Polymers90,0102
Non-polymers1,9915
Water3,549197
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.981, 126.981, 170.106
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 3 through 64 or resid 66...
d_2ens_1(chain "B" and (resid 3 through 64 or resid 66...
d_1ens_2chain "A" and 501
d_2ens_2chain "B" and 501
d_3ens_2chain "A" and 503
d_1ens_3chain "A" and 502
d_2ens_3chain "B" and 502

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ASPCYSA1 - 62
d_12ens_1PHELYSA66 - 79
d_13ens_1LEUPROA83 - 233
d_14ens_1GLYLYSA237 - 417
d_21ens_1ASPCYSB2 - 63
d_22ens_1PHELYSB65 - 78
d_23ens_1LEUPROB80 - 230
d_24ens_1GLYLYSB234 - 414
d_11ens_2THHTHHA501
d_21ens_2THHTHHB501
d_31ens_2THHTHHA503
d_11ens_3PLGPLGA502
d_21ens_3PLGPLGB502

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(0.606389638052, 0.0656199003907, 0.792455447035), (0.0686279713554, -0.997189388393, 0.0300586963162), (0.792200611216, 0.0361573277401, -0.609188672941)4.80253475568, 12.9764951459, -11.0266962259
2given(0.590030309568, 0.027067622029, 0.806927244322), (0.0688679136725, -0.997482682011, -0.0168970279566), (0.804438589488, 0.065541154438, -0.590409106313)4.45270205026, 11.6748041739, -9.8302648575
3given(0.787696764978, 0.345424117318, 0.510113698717), (0.221521807994, -0.931450008565, 0.288667577202), (0.574858152092, -0.114381207894, -0.810219133478)7.20953049502, -12.1652357308, -61.4496383785
4given(0.60508765874, 0.0608850811913, 0.793827394418), (0.07591750573, -0.996940679564, 0.0185960682667), (0.792531045174, 0.0490131443551, -0.6078587452)4.82133244964, 12.8159236041, -10.8871836889

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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-THH / N-[4-({[(6S)-2-AMINO-4-HYDROXY-5-METHYL-5,6,7,8-TETRAHYDROPTERIDIN-6-YL]METHYL}AMINO)BENZOYL]-L-GLUTAMIC ACID / 5-METHYLTETRAHYDROFOLATE


Mass: 459.456 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H25N7O6 / Feature type: SUBJECT OF INVESTIGATION
#3: 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.: 2 / Source method: obtained synthetically / Formula: C10H15N2O7P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 3.81 Å3/Da / Density % sol: 67.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 0.1M sodium cacodylate/hydrochloric acid pH 6.5, 2M ammonium sulfate, 0.2M sodium chloride

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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: 2.62→47.94 Å / Num. obs: 42482 / % possible obs: 99.92 % / Redundancy: 27 % / Biso Wilson estimate: 54.56 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.1274 / Rrim(I) all: 0.6592 / Net I/σ(I): 13.66
Reflection shellResolution: 2.62→2.714 Å / Mean I/σ(I) obs: 1.49 / Num. unique obs: 4171 / CC1/2: 0.54 / Rpim(I) all: 0.6547 / Rrim(I) all: 3.464

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Processing

Software
NameVersionClassification
BSSdata collection
XDSdata reduction
PHENIXphasing
Cootmodel building
PHENIX1.19.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7V3D

7v3d


Resolution: 2.62→47.94 Å / SU ML: 0.3455 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.8904
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1943 1999 4.71 %
Rwork0.1538 40483 -
obs0.1557 42482 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.41 Å2
Refinement stepCycle: LAST / Resolution: 2.62→47.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6269 0 139 197 6605
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00796568
X-RAY DIFFRACTIONf_angle_d1.00678917
X-RAY DIFFRACTIONf_chiral_restr0.05761002
X-RAY DIFFRACTIONf_plane_restr0.00591160
X-RAY DIFFRACTIONf_dihedral_angle_d19.48192459
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.506314884149
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.590635377006
ens_2d_3AX-RAY DIFFRACTIONTorsion NCS1.49635333177
ens_3d_2BX-RAY DIFFRACTIONTorsion NCS0.034175816183
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.62-2.680.35471370.27632797X-RAY DIFFRACTION97.96
2.68-2.760.26681420.24232858X-RAY DIFFRACTION100
2.76-2.840.30631400.23052846X-RAY DIFFRACTION100
2.84-2.930.29471400.20982835X-RAY DIFFRACTION100
2.93-3.030.22931410.19342859X-RAY DIFFRACTION100
3.03-3.160.22281420.18562869X-RAY DIFFRACTION100
3.16-3.30.24791410.18152839X-RAY DIFFRACTION100
3.3-3.470.20241410.16552873X-RAY DIFFRACTION100
3.47-3.690.21351430.14212896X-RAY DIFFRACTION100
3.69-3.970.16771440.12462894X-RAY DIFFRACTION99.97
3.97-4.370.14191430.11522901X-RAY DIFFRACTION100
4.38-5.010.13891440.11052925X-RAY DIFFRACTION100
5.01-6.310.15891460.14072972X-RAY DIFFRACTION100
6.31-47.940.19241550.15423119X-RAY DIFFRACTION99.76

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