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- PDB-7v3d: Complex structure of serine hydroxymethyltransferase from Enteroc... -

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Basic information

Entry
Database: PDB / ID: 7v3d
TitleComplex structure of serine hydroxymethyltransferase from Enterococcus faecium and its inhibitor
ComponentsSerine hydroxymethyltransferase
KeywordsTRANSFERASE / inhibitor / Antibacterial mechanism / complex
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 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain ...Serine hydroxymethyltransferase, pyridoxal phosphate binding site / Serine hydroxymethyltransferase pyridoxal-phosphate attachment site. / : / Serine hydroxymethyltransferase / Serine hydroxymethyltransferase-like domain / Serine hydroxymethyltransferase / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-5M5 / PYRIDOXAL-5'-PHOSPHATE / Serine hydroxymethyltransferase
Similarity search - Component
Biological speciesEnterococcus faecium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsHayashi, H. / Murayama, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
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
DepositionAug 10, 2021Deposition 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)91,3768
Polymers90,0102
Non-polymers1,3666
Water6,323351
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8560 Å2
ΔGint-69 kcal/mol
Surface area27300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.470, 119.470, 163.280
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-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 3.25 Å3/Da / Density % sol: 62.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: Na cacodylate trihydrate, Ammonium sulfate, Calcium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.28→48.21 Å / Num. obs: 54560 / % possible obs: 100 % / Redundancy: 16.8 % / Biso Wilson estimate: 38.97 Å2 / Rrim(I) all: 0.45 / Net I/σ(I): 8.12
Reflection shellResolution: 2.28→2.42 Å / Num. unique obs: 8764 / CC1/2: 0.57

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WXB

4wxb


Resolution: 2.28→48.21 Å / SU ML: 0.259 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.0296 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2086 1998 3.67 %
Rwork0.175 52469 -
obs0.1763 54467 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.86 Å2
Refinement stepCycle: LAST / Resolution: 2.28→48.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6241 0 92 351 6684
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00756460
X-RAY DIFFRACTIONf_angle_d1.05838771
X-RAY DIFFRACTIONf_chiral_restr0.0505991
X-RAY DIFFRACTIONf_plane_restr0.00541137
X-RAY DIFFRACTIONf_dihedral_angle_d4.06583833
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.340.31751400.28283686X-RAY DIFFRACTION99.92
2.34-2.40.32031410.26983680X-RAY DIFFRACTION100
2.4-2.470.30951400.26613691X-RAY DIFFRACTION100
2.47-2.550.28231410.23033692X-RAY DIFFRACTION99.95
2.55-2.640.26861410.21693697X-RAY DIFFRACTION99.95
2.64-2.750.26911400.20143687X-RAY DIFFRACTION99.97
2.75-2.870.23371420.20163742X-RAY DIFFRACTION99.97
2.87-3.020.24091420.19713700X-RAY DIFFRACTION99.97
3.02-3.210.22641420.19573745X-RAY DIFFRACTION99.95
3.21-3.460.18841420.16973732X-RAY DIFFRACTION99.97
3.46-3.810.20291430.15033764X-RAY DIFFRACTION99.95
3.81-4.360.17731450.13323782X-RAY DIFFRACTION99.97
4.36-5.490.15711460.13863846X-RAY DIFFRACTION100
5.49-48.210.16931530.15624025X-RAY DIFFRACTION99.88

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