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- PDB-9box: Room-temperature X-ray structure of human mitochondrial serine hy... -

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Basic information

Entry
Database: PDB / ID: 9box
TitleRoom-temperature X-ray structure of human mitochondrial serine hydroxymethyltransferase (hSHMT2) with PLP-glycine external aldimine and 5-formyltetrahydrofolate (folinic acid)
ComponentsSerine hydroxymethyltransferase, mitochondrial
KeywordsTRANSFERASE / PYRIDOXAL 5'-PHOSPHATE / PLP / FOLD TYPE 1 / ONE CARBON METABOLISM
Function / homology
Function and homology information


BRISC complex / formate biosynthetic process / L-allo-threonine aldolase activity / regulation of mitochondrial translation / glycine metabolic process / L-serine metabolic process / regulation of oxidative phosphorylation / L-serine biosynthetic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity ...BRISC complex / formate biosynthetic process / L-allo-threonine aldolase activity / regulation of mitochondrial translation / glycine metabolic process / L-serine metabolic process / regulation of oxidative phosphorylation / L-serine biosynthetic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / Metabolism of folate and pterines / tetrahydrofolate metabolic process / response to type I interferon / protein K63-linked deubiquitination / tetrahydrofolate interconversion / regulation of aerobic respiration / amino acid binding / mitochondrial nucleoid / RHOG GTPase cycle / one-carbon metabolic process / Mitochondrial protein degradation / protein tetramerization / pyridoxal phosphate binding / microtubule cytoskeleton / protein homotetramerization / mitochondrial inner membrane / mitochondrial matrix / positive regulation of cell population proliferation / chromatin binding / mitochondrion / extracellular exosome / identical protein binding / nucleus / cytoplasm
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-FFO / Serine hydroxymethyltransferase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsDrago, V.N. / Kovalevsky, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM137008 United States
CitationJournal: Chem Sci / Year: 2024
Title: Universality of critical active site glutamate as an acid-base catalyst in serine hydroxymethyltransferase function.
Authors: Drago, V.N. / Phillips, R.S. / Kovalevsky, A.
History
DepositionMay 6, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)208,42812
Polymers205,3184
Non-polymers3,1118
Water13,781765
1
A: Serine hydroxymethyltransferase, mitochondrial
C: Serine hydroxymethyltransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,2146
Polymers102,6592
Non-polymers1,5554
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11520 Å2
ΔGint-49 kcal/mol
Surface area30870 Å2
MethodPISA
2
B: Serine hydroxymethyltransferase, mitochondrial
D: Serine hydroxymethyltransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,2146
Polymers102,6592
Non-polymers1,5554
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11340 Å2
ΔGint-52 kcal/mol
Surface area30900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.980, 119.300, 134.627
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221

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Components

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


Mass: 51329.453 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SHMT2 / Production host: Escherichia coli (E. coli)
References: UniProt: P34897, glycine hydroxymethyltransferase
#2: Chemical
ChemComp-A1AQW / (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)glycine


Mass: 304.193 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H13N2O7P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-FFO / N-[4-({[(6S)-2-amino-5-formyl-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid / [6S]-5-FORMYL-TETRAHYDROFOLATE / 6S-FOLINIC ACID


Mass: 473.439 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H23N7O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 765 / 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: 2.8 Å3/Da / Density % sol: 56.11 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.6 / Details: 0.5 M Gly pH 8.6, 10 mM folinic acid, 18% PEG 3350

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 24, 2023
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 125654 / % possible obs: 93.4 % / Redundancy: 4.4 % / CC1/2: 0.987 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.062 / Net I/σ(I): 12.9
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.739 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 6402 / CC1/2: 0.483 / Rpim(I) all: 0.427

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→42.82 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1 / Phase error: 20.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1886 6066 4.97 %
Rwork0.1623 --
obs0.1636 122017 90.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→42.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14292 0 216 765 15273
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00914828
X-RAY DIFFRACTIONf_angle_d0.97320066
X-RAY DIFFRACTIONf_dihedral_angle_d16.2725572
X-RAY DIFFRACTIONf_chiral_restr0.0512184
X-RAY DIFFRACTIONf_plane_restr0.0142628
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.120.27491710.25093412X-RAY DIFFRACTION80
2.12-2.150.23632030.23163532X-RAY DIFFRACTION84
2.15-2.170.25161680.23373605X-RAY DIFFRACTION85
2.17-2.20.25581810.22873676X-RAY DIFFRACTION87
2.2-2.230.25341990.23233717X-RAY DIFFRACTION88
2.23-2.260.27362090.22113774X-RAY DIFFRACTION89
2.26-2.290.26342110.21543854X-RAY DIFFRACTION91
2.29-2.330.22161920.21163879X-RAY DIFFRACTION92
2.33-2.360.24571880.21273928X-RAY DIFFRACTION92
2.36-2.40.26471940.21163892X-RAY DIFFRACTION92
2.4-2.440.23381970.20533946X-RAY DIFFRACTION92
2.44-2.490.22812140.20323927X-RAY DIFFRACTION93
2.49-2.540.24152030.20223954X-RAY DIFFRACTION93
2.54-2.590.21452020.20053946X-RAY DIFFRACTION93
2.59-2.640.22522210.19463948X-RAY DIFFRACTION93
2.65-2.710.24822250.18663937X-RAY DIFFRACTION93
2.71-2.770.22272240.17953948X-RAY DIFFRACTION93
2.77-2.850.22122240.17723924X-RAY DIFFRACTION93
2.85-2.930.19852230.17123945X-RAY DIFFRACTION93
2.93-3.030.19531680.16164002X-RAY DIFFRACTION93
3.03-3.140.19972150.16283942X-RAY DIFFRACTION93
3.14-3.260.18411960.15273969X-RAY DIFFRACTION92
3.26-3.410.17671970.14553957X-RAY DIFFRACTION92
3.41-3.590.15722080.13283948X-RAY DIFFRACTION92
3.59-3.810.14681970.12223901X-RAY DIFFRACTION91
3.81-4.110.12581920.11553944X-RAY DIFFRACTION91
4.11-4.520.13122060.11253882X-RAY DIFFRACTION90
4.52-5.170.13532190.11563894X-RAY DIFFRACTION89
5.18-6.520.16112090.14173860X-RAY DIFFRACTION89
6.52-42.820.14262100.13093908X-RAY DIFFRACTION86

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