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- PDB-9j4h: Crystal structure of SHMT apo form -

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Basic information

Entry
Database: PDB / ID: 9j4h
TitleCrystal structure of SHMT apo form
ComponentsSerine hydroxymethyltransferase
KeywordsTRANSFERASE / One carbon metabolism / apo enzyme PLP
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
TRIETHYLENE GLYCOL / Serine hydroxymethyltransferase
Similarity search - Component
Biological speciesEnterococcus faecium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsMurayama, K. / Hayashi, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP23K07918 Japan
CitationJournal: Arch.Biochem.Biophys. / Year: 2024
Title: SHIN-2 exerts potent activity against VanA-type vancomycin-resistant Enterococcus faecium in vitro by stabilizing the active site loop of serine hydroxymethyltransferase.
Authors: Hayashi, H. / Saijo, E. / Hirata, K. / Murakami, S. / Okuda, H. / Kodama, E.N. / Hasegawa, K. / Murayama, K.
History
DepositionAug 9, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)181,5338
Polymers180,9334
Non-polymers6014
Water15,133840
1
A: Serine hydroxymethyltransferase
B: Serine hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,7674
Polymers90,4662
Non-polymers3002
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7320 Å2
ΔGint-36 kcal/mol
Surface area28420 Å2
MethodPISA
2
C: Serine hydroxymethyltransferase
D: Serine hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,7674
Polymers90,4662
Non-polymers3002
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7800 Å2
ΔGint-33 kcal/mol
Surface area28460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)276.920, 68.090, 95.340
Angle α, β, γ (deg.)90.000, 110.605, 90.000
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11C-742-

HOH

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Components

#1: Protein
Serine hydroxymethyltransferase / SHMT / Serine methylase


Mass: 45233.152 Da / Num. of mol.: 4
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-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 840 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.34 Å3/Da / Density % sol: 47.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 17.5% PEG3350, 1 mM nitrophenol, 0.225 M sodium thiocyanate

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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: Jul 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.04→47.67 Å / Num. obs: 105322 / % possible obs: 99.9 % / Redundancy: 11.1 % / Biso Wilson estimate: 34.77 Å2 / CC1/2: 0.993 / Net I/σ(I): 7.2
Reflection shellResolution: 2.04→2.16 Å / Num. unique obs: 16500 / CC1/2: 0.567

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7V3D

7v3d


Resolution: 2.04→47.67 Å / SU ML: 0.262 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.4842 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2098 2013 1.92 %
Rwork0.1957 102968 -
obs0.196 104981 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.49 Å2
Refinement stepCycle: LAST / Resolution: 2.04→47.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12503 0 100 840 13443
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002812846
X-RAY DIFFRACTIONf_angle_d0.583417405
X-RAY DIFFRACTIONf_chiral_restr0.04111979
X-RAY DIFFRACTIONf_plane_restr0.00372265
X-RAY DIFFRACTIONf_dihedral_angle_d19.94424669
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.04-2.090.33561240.32236324X-RAY DIFFRACTION85.2
2.09-2.150.2871410.29617371X-RAY DIFFRACTION99.96
2.15-2.210.31911450.26937394X-RAY DIFFRACTION99.87
2.21-2.280.27391430.25467364X-RAY DIFFRACTION99.97
2.28-2.360.27321470.2467388X-RAY DIFFRACTION99.99
2.36-2.460.25681440.23567407X-RAY DIFFRACTION99.95
2.46-2.570.28991440.22947394X-RAY DIFFRACTION100
2.57-2.710.23261460.21797411X-RAY DIFFRACTION100
2.71-2.880.24011420.20647423X-RAY DIFFRACTION99.99
2.88-3.10.22141440.20387459X-RAY DIFFRACTION100
3.1-3.410.19421450.20237424X-RAY DIFFRACTION100
3.41-3.90.18051480.1697456X-RAY DIFFRACTION99.97
3.9-4.920.17481470.15397516X-RAY DIFFRACTION100
4.92-47.670.15331530.15877637X-RAY DIFFRACTION99.82

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